Contacts of the helix formed by residues 302 - 327 (chain C) in PDB entry 3EXG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 302 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C PHE* 3.5 18.2 - - - -
296C VAL* 4.2 2.5 - - - -
301C ALA* 1.3 72.2 - - - +
303C VAL* 1.3 60.0 + - - +
304C GLU* 3.6 14.4 + - - +
305C GLU* 2.7 47.3 + - - +
306C LEU* 2.8 31.4 + - - +
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Residues in contact with VAL 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C LYS* 4.2 24.8 - - - +
296C VAL* 3.9 21.5 - - + +
302C SER* 1.3 72.5 - - - +
304C GLU* 1.3 82.4 + - + +
306C LEU* 3.4 5.7 + - - +
307C LYS* 2.6 37.2 + - + +
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Residues in contact with GLU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C SER* 3.1 10.6 + - - +
303C VAL* 1.3 103.0 - - + +
305C GLU* 1.3 58.4 + - - +
307C LYS* 3.0 9.9 + - + +
308C GLU* 2.8 39.9 + - + +
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Residues in contact with GLU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C PHE* 3.1 14.8 - - + -
29C ARG* 3.3 24.8 + - - -
33C LEU* 5.2 7.0 - - + +
301C ALA* 3.0 20.7 - - + +
302C SER* 2.7 52.9 + - - +
304C GLU* 1.3 71.6 - - - +
306C LEU* 1.3 63.2 + - + +
308C GLU* 3.2 27.2 + - - +
309C ILE* 3.3 17.7 + - + +
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Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.3 15.7 - - + -
36C TYR* 4.0 32.7 - - + +
292C LYS* 3.8 44.4 - - + +
295C MET* 4.7 13.9 - - + -
296C VAL* 4.8 5.8 - - + -
301C ALA* 4.4 9.6 - - + -
302C SER 2.8 18.9 + - - +
303C VAL* 3.6 8.3 - - - +
305C GLU* 1.3 72.4 - - - +
307C LYS* 1.3 64.3 + - - +
308C GLU 3.1 1.4 + - - -
309C ILE* 3.1 33.5 + - + +
310C ASP* 3.1 18.8 + - - +
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Residues in contact with LYS 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C LYS* 5.9 3.8 - - - +
303C VAL* 2.6 26.5 + - + +
304C GLU* 3.0 12.7 + - + +
306C LEU* 1.3 70.3 - - - +
308C GLU* 1.3 57.9 + - - +
310C ASP* 3.2 38.2 + - - +
311C VAL* 3.0 28.0 + - + +
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Residues in contact with GLU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C GLU* 2.8 27.3 + - - +
305C GLU* 3.2 21.4 + - - +
306C LEU 3.1 0.4 - - - -
307C LYS* 1.3 76.1 - - + +
309C ILE* 1.3 62.2 + - + +
310C ASP 3.2 2.0 - - - -
311C VAL* 3.0 23.5 + - + +
312C GLU* 3.0 24.0 + - + +
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Residues in contact with ILE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.6 23.3 - - + +
36C TYR* 3.7 29.4 - - + -
37C ARG* 2.9 52.7 - - + +
40C GLN* 6.1 0.7 - - - -
305C GLU 3.3 14.8 - - - +
306C LEU* 3.1 19.7 + - + +
308C GLU* 1.3 72.9 - - + +
310C ASP* 1.3 65.7 + - - +
312C GLU* 3.1 6.9 + - + +
313C VAL* 2.9 28.5 + - + +
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Residues in contact with ASP 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C TYR* 2.8 32.6 + - - -
40C GLN* 3.5 22.5 - - - +
44C ARG* 6.1 0.2 - - - +
292C LYS* 5.2 4.2 - - - -
306C LEU* 3.1 15.0 + - - +
307C LYS* 3.2 41.5 - - - +
309C ILE* 1.3 76.5 - - - +
311C VAL* 1.3 59.5 + - + +
313C VAL* 3.7 1.4 + - - +
314C ARG* 3.2 28.3 + - - +
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Residues in contact with VAL 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C LYS* 3.0 23.3 - - + +
308C GLU* 3.0 12.7 + - - +
310C ASP* 1.3 75.5 - - + +
312C GLU* 1.3 62.8 + - + +
314C ARG* 3.5 8.1 - - + +
315C LYS* 3.4 24.8 + - - +
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Residues in contact with GLU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ARG* 3.1 31.8 + - - +
308C GLU* 3.1 22.4 - - - +
309C ILE* 3.4 11.1 - - + +
311C VAL* 1.3 75.5 - - + +
313C VAL* 1.3 60.6 + - - +
315C LYS* 3.0 22.0 + - - +
316C GLU* 3.0 11.7 + - - +
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Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ARG* 4.1 25.6 - - + +
40C GLN* 4.2 10.3 - - + +
41C THR* 3.3 37.2 - - + +
44C ARG* 3.5 32.3 - - + -
309C ILE* 2.9 19.1 + - + +
310C ASP 4.3 1.8 - - - +
312C GLU* 1.3 71.5 - - - +
314C ARG* 1.3 69.1 + - - +
315C LYS 2.9 1.6 - - - -
316C GLU* 2.8 10.6 + - + +
317C ILE* 2.8 28.0 + - + +
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Residues in contact with ARG 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 3.3 39.6 - - - +
310C ASP* 3.2 22.8 + - - +
311C VAL* 3.5 11.7 - - + +
313C VAL* 1.3 79.1 - - - +
315C LYS* 1.3 57.4 + - - +
317C ILE* 3.8 8.3 + - - +
318C GLU* 2.9 36.0 + - + +
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Residues in contact with LYS 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C VAL* 3.4 13.4 + - - +
312C GLU* 3.0 12.2 + - - +
313C VAL 2.9 0.8 - - - -
314C ARG* 1.3 78.7 - - - +
316C GLU* 1.3 62.3 + - - +
318C GLU* 3.2 9.2 + - + +
319C ASP* 2.8 52.6 + - - +
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Residues in contact with GLU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR* 6.0 3.1 - - + -
102C VAL* 4.9 13.8 - - + +
103C ARG* 5.9 0.8 - - - -
312C GLU 3.0 10.9 + - - +
313C VAL* 2.8 19.0 + - + +
315C LYS* 1.3 72.9 - - - +
317C ILE* 1.3 62.0 + - + +
319C ASP* 3.4 18.4 + - - +
320C ALA* 3.0 28.8 + - - +
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Residues in contact with ILE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C THR* 4.1 8.7 - - + +
44C ARG* 3.5 25.4 - - + +
45C MET* 3.8 20.4 - - + +
48C LYS* 3.7 41.3 - - + -
102C VAL* 3.7 28.0 - - + -
106C LEU* 5.1 1.3 - - + -
313C VAL* 2.8 26.0 + - + +
314C ARG* 3.9 9.0 - - - +
316C GLU* 1.3 73.0 - - + +
318C GLU* 1.3 60.0 + - - +
320C ALA* 3.1 4.9 + - - +
321C ALA* 2.8 28.2 + - - +
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LYS* 3.9 25.0 + - - -
314C ARG* 2.9 29.3 + - + +
315C LYS* 3.2 12.8 + - + +
317C ILE* 1.3 78.3 - - - +
319C ASP* 1.3 60.5 + - - +
321C ALA* 4.5 6.1 - - - +
322C GLN* 3.1 28.1 + - + +
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Residues in contact with ASP 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ARG* 4.5 14.7 + - - +
315C LYS* 2.8 49.6 + - - +
316C GLU* 3.5 18.6 - - - +
318C GLU* 1.3 71.3 - - - +
320C ALA* 1.3 58.1 + - - +
322C GLN* 3.1 12.5 - - - +
323C PHE* 3.1 25.3 + - - +
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C VAL* 3.8 15.7 - - + -
103C ARG* 3.7 41.0 - - + +
106C LEU* 4.1 6.3 - - + -
316C GLU* 3.0 18.5 + - + +
317C ILE 3.6 2.9 - - - +
319C ASP* 1.3 72.5 - - - +
321C ALA* 1.3 56.7 + - - +
322C GLN 3.1 1.8 - - - -
323C PHE* 3.0 3.5 + - - +
324C ALA* 2.7 36.4 + - - +
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Residues in contact with ALA 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LYS* 3.6 37.9 - - + +
52C LEU* 4.8 8.3 - - + -
106C LEU* 3.8 8.2 - - + +
317C ILE 2.8 19.4 + - - +
318C GLU* 4.2 8.3 - - - +
320C ALA* 1.3 72.5 - - - +
322C GLN* 1.3 52.2 + - - +
324C ALA* 3.7 3.3 - - - -
325C THR* 2.7 41.9 + - + +
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Residues in contact with GLN 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C GLU* 3.1 20.7 + - + +
319C ASP* 3.1 15.3 - - - +
321C ALA* 1.3 76.8 - - - +
323C PHE* 1.3 65.4 + - + +
325C THR* 3.5 4.8 + - - -
326C ALA* 3.1 32.6 + - - +
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Residues in contact with PHE 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ARG* 3.4 65.5 - - + +
104C GLU* 5.0 0.4 - - + -
107C ALA* 3.7 21.5 - - + -
114C GLY* 3.8 26.5 - - - -
319C ASP 3.1 8.7 + - - +
320C ALA 3.0 9.6 + - - +
322C GLN* 1.3 82.2 - - + +
324C ALA* 1.3 59.0 + - - +
326C ALA* 4.1 1.7 - - - +
327C ASP* 2.9 51.8 + - + +
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 5.2 1.3 - - + -
103C ARG 4.7 1.1 - - - +
106C LEU* 3.7 15.0 - - + -
107C ALA* 3.5 34.5 - - + +
110C THR* 2.7 33.3 + - + +
112C ARG* 3.5 9.5 + - - +
320C ALA 2.7 20.0 + - - +
321C ALA* 3.9 5.4 - - - +
323C PHE* 1.3 74.4 - - - +
325C THR* 1.3 59.8 + - + +
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Residues in contact with THR 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 4.3 28.0 - - + -
55C GLN* 6.0 0.2 - - - +
57C ILE* 4.4 19.1 - - + -
110C THR* 4.7 0.4 - - + -
112C ARG* 3.1 24.5 + - - +
321C ALA* 2.7 23.9 + - + +
322C GLN* 3.5 7.3 + - - -
324C ALA* 1.3 79.3 - - - +
326C ALA* 1.3 56.4 + - - +
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Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ARG* 4.3 0.4 - - - -
322C GLN* 3.1 33.0 + - - +
323C PHE* 4.1 2.7 - - - +
325C THR* 1.3 78.5 - - - +
327C ASP* 1.3 64.4 + - - +
328C PRO* 3.4 8.7 - - - +
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Residues in contact with ASP 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ALA* 5.6 0.2 - - + -
112C ARG* 2.8 37.5 + - + +
113C LYS* 3.2 19.0 + - - +
114C GLY* 2.5 39.9 + - - -
323C PHE* 2.9 35.6 + - + +
324C ALA* 5.2 0.2 - - - -
325C THR 3.6 0.4 - - - -
326C ALA* 1.3 76.7 - - - +
328C PRO* 1.3 80.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il