Contacts of the helix formed by residues 311 - 326 (chain C) in PDB entry 4D2W
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 ASP 311 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C TYR 3.9 1.7 - - - +
74C HIS* 3.6 12.4 - - - -
75C VAL 5.1 1.1 - - - -
309C GLN* 3.2 32.6 + - + +
310C TYR* 1.3 81.0 - - - +
312C HIS* 1.3 64.6 + - - +
313C LEU* 3.4 15.7 + - - +
314C THR* 3.1 30.0 + - - -
315C ALA 3.2 9.0 + - - -
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Residues in contact with HIS 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 3.4 54.6 - + + +
30C HIS* 3.0 36.6 + + - -
32C LEU* 3.6 23.9 - - + +
74C HIS* 3.5 22.7 + - + +
293C HIS* 6.1 1.3 - + - -
311C ASP* 1.3 75.8 - - - +
313C LEU* 1.3 53.6 + - - +
315C ALA* 3.4 1.7 + - - +
316C THR* 2.7 48.8 + - - -
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Residues in contact with LEU 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C LEU* 3.8 20.0 - - + -
294C HIS* 4.1 12.8 - - + +
301C MET* 3.5 26.0 - - + -
304C LEU* 3.7 48.9 - - + +
305C ILE* 3.8 18.6 - - + +
311C ASP* 3.2 15.4 + - - +
312C HIS* 1.3 76.0 - - - +
314C THR* 1.3 60.5 + - - +
316C THR* 3.3 3.7 + - - -
317C TYR* 2.9 28.6 + - - +
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Residues in contact with THR 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C TYR 3.6 11.2 - - - +
305C ILE* 5.1 1.7 + - - -
308C TRP* 3.9 24.3 - - + -
309C GLN 3.5 8.7 + - - -
310C TYR* 3.1 52.9 + - + +
311C ASP* 3.1 7.6 + - - -
313C LEU* 1.3 76.9 - - - +
315C ALA* 1.3 56.3 + - - +
317C TYR* 3.5 3.8 + - - +
318C LEU* 2.9 51.9 + - + +
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Residues in contact with ALA 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 3.5 24.7 - - - +
30C HIS* 4.3 9.4 - - + +
73C TYR* 3.3 29.5 + - + +
74C HIS* 4.0 7.2 - - + +
311C ASP 3.2 7.1 + - - +
312C HIS* 3.5 8.1 - - - +
313C LEU 3.3 0.2 - - - -
314C THR* 1.3 76.1 - - - +
316C THR* 1.4 56.4 + - - +
318C LEU* 3.9 0.7 - - - +
319C LEU* 3.0 39.3 + - + +
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Residues in contact with THR 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C HIS* 3.4 24.4 + - + -
32C LEU* 4.4 8.7 - - + -
33C THR* 4.1 1.5 - - + +
290C LEU* 3.6 22.9 - - + -
312C HIS* 2.7 35.6 + - - -
313C LEU* 3.3 4.7 + - - -
315C ALA* 1.4 71.3 - - - +
317C TYR* 1.3 61.8 + - - +
319C LEU 3.9 0.3 - - - -
320C LEU* 3.0 31.5 + - - +
332C LEU* 3.5 33.0 - - + -
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Residues in contact with TYR 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ARG* 5.5 0.2 - - - -
278C PRO 5.9 0.9 - - - -
281C HIS 4.3 3.2 + - - -
282C LEU* 3.5 12.7 - - + +
283C ASP* 2.8 37.4 + - + +
286C CYS* 3.6 23.5 - - + -
287C VAL* 4.3 9.0 - - + -
290C LEU* 3.8 28.4 - - + +
305C ILE* 3.9 21.5 - - + -
308C TRP* 3.7 32.1 - + - -
313C LEU 2.9 17.2 + - - +
314C THR* 4.0 3.1 - - - +
316C THR* 1.3 76.2 - - - +
318C LEU* 1.3 65.9 + - + +
320C LEU* 3.4 3.3 + - - +
321C LEU* 3.0 51.3 + - + +
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ARG* 4.0 33.0 - - - +
71C GLN* 3.7 28.5 - - + +
72C LEU 3.9 8.3 - - - +
73C TYR* 3.7 22.6 - - + -
308C TRP* 4.5 2.0 - - + -
314C THR* 2.9 38.9 + - + +
317C TYR* 1.3 94.2 - - + +
319C LEU* 1.3 58.2 + - - +
321C LEU* 3.5 17.0 + - + +
322C ALA* 3.1 24.1 + - - +
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Residues in contact with LEU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 5.3 0.7 - - + -
30C HIS* 3.6 39.0 - - + +
33C THR* 3.8 18.8 - - + +
35C GLU* 3.8 23.0 - - + +
36C MET 4.7 3.4 - - - +
37C VAL* 3.9 15.7 - - + -
73C TYR* 3.5 40.2 - - + +
315C ALA* 3.0 25.0 + - + +
318C LEU* 1.3 74.8 - - - +
320C LEU* 1.4 56.4 + - - +
322C ALA* 3.2 9.0 + - + +
323C LYS* 2.8 33.1 + - - +
326C ARG* 6.1 1.1 - - - +
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C THR* 4.0 5.0 - - + +
286C CYS* 3.8 31.7 - - + +
289C GLU* 3.9 23.6 - - + -
290C LEU* 4.4 10.5 - - + -
316C THR 3.0 14.3 + - - +
317C TYR* 3.6 5.2 - - - +
319C LEU* 1.4 73.4 - - - +
321C LEU* 1.4 60.0 + - - +
323C LYS* 3.3 12.1 + - + +
324C LYS* 3.0 29.6 + - - +
330C VAL* 3.8 12.6 - - + +
331C ARG 3.6 38.1 - - - +
332C LEU* 3.8 23.3 - - + -
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ASN* 6.1 4.0 - - + +
278C PRO* 5.4 13.0 - - + -
283C ASP* 3.7 36.8 - - + +
286C CYS* 3.6 9.7 - - - -
317C TYR* 3.0 38.1 + - + +
318C LEU* 3.5 18.4 - - + +
320C LEU* 1.4 74.6 - - - +
322C ALA* 1.4 56.6 + - - +
324C LYS* 3.5 7.6 - - + +
325C ALA* 3.0 26.5 + - - +
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU* 4.7 4.3 - - - +
73C TYR* 5.1 5.2 - - - +
318C LEU 3.1 13.9 + - - +
319C LEU* 3.2 17.6 + - + +
321C LEU* 1.4 73.8 - - - +
323C LYS* 1.3 65.4 + - - +
325C ALA* 3.1 17.3 + - - +
326C ARG* 3.1 45.6 + - - +
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Residues in contact with LYS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C THR* 2.8 41.7 + - - +
35C GLU* 3.6 22.8 + - - +
319C LEU 2.8 14.8 + - - +
320C LEU* 3.4 16.4 - - + +
322C ALA* 1.3 74.8 - - - +
324C LYS* 1.3 61.5 + - - +
326C ARG* 3.1 13.8 + - - +
328C LYS* 3.3 41.2 + - + +
329C PRO 3.3 21.9 + - - +
331C ARG* 3.0 25.4 + - - +
333C ARG* 4.5 9.5 - - - +
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Residues in contact with LYS 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C ASP* 2.9 38.4 + - - +
285C ASP* 3.4 24.0 - - + +
286C CYS* 4.6 1.3 - - - -
320C LEU 3.0 16.2 + - - +
321C LEU* 3.5 10.0 - - + +
323C LYS* 1.3 72.8 - - - +
325C ALA* 1.4 63.2 + - - +
327C GLY* 3.1 15.2 + - - -
328C LYS 4.0 10.7 + - - +
330C VAL* 3.8 24.1 - - + +
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Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C TYR* 4.9 3.1 + - - -
321C LEU 3.0 14.6 + - - +
322C ALA* 3.1 12.7 + - - +
324C LYS* 1.4 75.0 - - - +
326C ARG* 1.3 67.2 + - - +
327C GLY* 3.3 2.5 + - - -
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Residues in contact with ARG 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU* 4.4 12.3 + - - -
73C TYR* 5.6 3.6 + - - -
87C GLU* 4.9 14.3 + - - +
141C ASP* 5.1 5.3 + - - -
142C GLU* 3.6 33.0 + - - +
143C TYR* 3.3 39.9 + - + +
147C LYS* 6.1 0.4 - - - +
319C LEU* 6.1 0.8 - - - +
322C ALA* 3.1 38.7 + - - +
323C LYS* 3.1 10.4 + - - +
325C ALA* 1.3 82.3 - - - +
327C GLY* 1.3 56.3 + - - +
328C LYS* 3.3 14.4 + - + +
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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