Contacts of the helix formed by residues 292 - 309 (chain C) in PDB entry 1EFA
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 292 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C PHE* 3.2 16.2 - - + -
290C LYS* 3.9 24.3 + - + +
291C GLN* 1.3 65.9 - - - +
293C PHE* 1.3 64.0 + - - +
294C ARG* 3.0 23.2 + - - +
295C LEU* 3.1 36.6 + - + +
296C LEU 3.2 9.4 + - - -
320C PRO 5.3 1.5 + - - +
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Residues in contact with PHE 293 (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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74C HIS* 4.1 20.9 - + - -
75C ALA* 3.6 18.4 - - + -
78C GLN* 3.7 33.9 - - + -
79C ILE* 4.1 19.3 - - + +
82C ALA* 3.8 6.1 - - - +
161C PHE* 4.3 3.1 - + - -
274C ASP* 3.7 32.5 - - + -
276C THR* 5.4 2.0 - - + -
291C GLN* 2.9 30.2 + - + -
292C ASP* 1.3 69.5 + - - +
294C ARG* 1.3 65.7 + - - +
296C LEU* 3.3 5.6 + - - +
297C GLY* 3.1 18.9 + - - -
903C NPF 3.3 35.4 - - + -
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Residues in contact with ARG 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLN 5.5 0.6 + - - -
81C ALA* 3.6 10.5 + - - +
82C ALA* 3.3 42.8 - - - +
85C SER* 3.3 28.9 + - - -
292C ASP* 3.0 11.5 + - - +
293C PHE* 1.3 76.8 - - - +
295C LEU* 1.3 54.7 + - - +
297C GLY 3.2 2.1 + - - -
298C GLN* 2.8 37.5 + - - +
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C PHE* 5.1 2.5 - - + -
292C ASP* 3.1 32.5 + - + +
294C ARG* 1.3 80.7 - - - +
296C LEU* 1.3 55.4 + - - +
298C GLN* 3.7 16.8 - - - +
299C THR* 2.7 50.6 + - - +
319C LEU* 4.2 21.5 - - + -
320C PRO* 4.6 18.8 - - + +
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Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 3.5 33.0 - - + -
148C LEU* 4.0 14.8 - - + -
159C ILE* 3.9 25.8 - - + +
160C ILE* 5.1 2.0 - - - -
161C PHE* 3.8 31.6 - - + -
292C ASP 3.2 3.8 + - - -
293C PHE 3.6 7.9 - - - +
294C ARG 3.2 0.2 - - - -
295C LEU* 1.3 79.0 - - - +
297C GLY* 1.3 54.9 + - - +
299C THR* 3.7 0.9 - - - -
300C SER* 2.6 48.5 + - - +
319C LEU* 3.6 23.5 - - + +
903C NPF 4.2 10.8 - - + +
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Residues in contact with GLY 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ILE* 4.2 4.9 - - - +
82C ALA* 3.8 21.1 - - - -
83C ILE* 3.9 17.5 - - - +
293C PHE 3.1 11.7 + - - -
294C ARG 3.7 2.7 - - - -
296C LEU* 1.3 76.9 - - - +
298C GLN* 1.3 63.8 + - - +
300C SER* 3.3 4.2 + - - -
301C VAL* 3.2 28.2 + - - +
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Residues in contact with GLN 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ALA* 4.2 2.2 + - + +
86C ARG* 3.5 41.9 - - + +
294C ARG 2.8 21.5 + - - +
295C LEU* 3.7 25.3 - - - +
297C GLY* 1.3 73.4 - - - +
299C THR* 1.3 70.4 + - - +
301C VAL 3.4 0.5 + - - -
302C ASP* 2.6 51.0 + - - +
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Residues in contact with THR 299 (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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159C ILE* 3.7 19.3 - - + -
295C LEU* 2.7 39.4 + - - +
296C LEU* 3.8 3.8 - - - -
298C GLN* 1.3 83.9 + - - +
300C SER* 1.3 60.5 + - - +
302C ASP* 3.8 2.7 - - + +
303C ARG* 2.9 30.6 + - + +
317C GLN* 3.9 23.8 - - - +
319C LEU* 4.6 8.6 - - + +
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Residues in contact with SER 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ILE* 4.7 2.2 - - - -
123C ILE* 3.9 18.5 - - - +
146C LEU* 3.5 17.2 - - - +
148C LEU* 3.5 31.7 - - - +
159C ILE* 4.0 2.8 - - - +
296C LEU* 2.6 27.8 + - - +
297C GLY* 3.6 8.7 - - - -
298C GLN 3.3 0.4 - - - -
299C THR* 1.3 77.4 - - - +
301C VAL* 1.3 56.2 + - - +
303C ARG 3.5 0.2 + - - -
304C LEU* 2.9 30.0 + - - +
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Residues in contact with VAL 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 3.8 24.0 - - + -
83C ILE* 3.6 42.0 - - + +
86C ARG* 3.4 24.5 - - + -
87C ALA* 4.2 8.5 - - + +
90C LEU* 3.8 16.4 - - + -
92C ALA* 5.4 0.4 - - + -
123C ILE* 4.5 5.2 - - + -
297C GLY 3.2 12.9 + - - +
300C SER* 1.3 73.6 - - - +
302C ASP* 1.3 69.5 + - - +
304C LEU* 3.2 3.6 + - - +
305C LEU* 3.0 26.9 + - + +
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Residues in contact with ASP 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ARG* 3.2 39.9 + - - -
90C LEU* 3.6 4.8 - - - +
298C GLN* 2.6 33.8 + - - +
299C THR* 3.8 5.2 - - + +
301C VAL* 1.3 75.2 - - - +
303C ARG* 1.3 57.4 + - - +
305C LEU* 3.4 8.3 + - - +
306C GLN* 3.1 41.9 + - - +
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Residues in contact with ARG 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LEU* 3.5 34.6 - - + +
157C ASN* 4.2 5.9 - - - +
158C SER 3.1 12.8 + - - -
159C ILE* 3.4 9.4 - - + +
299C THR* 2.9 20.0 + - + +
302C ASP* 1.3 74.7 - - - +
304C LEU* 1.3 65.1 + - - +
306C GLN* 3.2 24.0 + - - +
307C LEU* 3.0 27.8 + - + +
313C VAL* 3.3 31.7 + - - +
315C GLY 3.7 17.4 + - - -
316C ASN 4.3 1.0 - - - -
317C GLN* 2.7 54.1 + - - +
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 3.5 41.3 - - + -
120C SER* 6.1 0.2 - - - +
121C GLY* 3.6 23.3 - - - -
122C LEU 3.3 20.0 - - - +
123C ILE* 3.8 12.3 - - + -
144C PRO* 3.8 24.7 - - + +
145C ALA 4.7 0.4 - - - -
146C LEU* 4.3 11.7 - - + -
300C SER 2.9 19.5 + - - +
301C VAL* 3.2 3.6 + - - +
303C ARG* 1.3 76.5 - - - +
305C LEU* 1.3 59.3 + - + +
307C LEU* 3.6 7.0 + - + +
308C SER* 3.0 26.0 + - - -
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Residues in contact with LEU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 3.9 39.7 - - + -
64C ILE* 4.1 20.6 - - + -
90C LEU* 3.4 36.3 - - + -
92C ALA* 4.9 2.5 - - + -
120C SER* 5.6 1.8 - - - +
301C VAL* 3.0 24.3 + - + +
302C ASP* 3.6 4.9 - - - +
304C LEU* 1.3 75.9 - - + +
306C GLN* 1.3 67.3 + - - +
308C SER* 3.0 12.8 + - - -
309C GLN* 3.0 33.2 + - - +
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Residues in contact with GLN 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ASP* 3.1 26.3 + - - +
303C ARG* 3.6 17.6 + - - +
305C LEU* 1.3 75.4 - - - +
307C LEU* 1.3 57.6 + - - +
309C GLN* 2.9 21.5 + - - -
311C GLN* 3.0 56.6 + - + +
313C VAL* 3.6 30.2 - - + +
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C PRO* 3.9 20.8 - - + +
145C ALA 4.4 6.3 - - - +
146C LEU* 4.5 3.6 - - + -
157C ASN* 3.9 27.6 - - + +
303C ARG* 3.0 32.7 + - + +
304C LEU* 3.7 13.5 - - + +
306C GLN* 1.3 76.3 - - - +
308C SER* 1.3 57.2 + - - +
310C GLY* 2.8 22.9 + - - +
311C GLN 4.3 7.6 - - - +
313C VAL* 3.7 28.3 - - + +
314C LYS* 4.0 30.4 + - + +
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Residues in contact with SER 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C SER* 3.3 33.5 + - - -
144C PRO* 3.9 11.6 - - - +
304C LEU* 3.0 15.2 + - - -
305C LEU* 3.0 20.1 + - - -
307C LEU* 1.3 76.2 - - - +
309C GLN* 1.3 57.1 + - - +
310C GLY 3.4 2.9 + - - -
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Residues in contact with GLN 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 6.1 3.0 - - - +
305C LEU* 3.0 20.6 + - - +
306C GLN* 2.9 11.8 + - - +
308C SER* 1.3 78.9 - - - +
310C GLY* 1.3 55.5 + - - +
311C GLN* 2.8 24.8 + - + +
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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