Contacts of the helix formed by residues 261 - 275 (chain C) in PDB entry 6GL7
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 261 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU* 5.5 4.9 - - - +
257C VAL 4.9 1.3 - - - +
258C CYS* 2.9 9.2 + - - +
259C ARG 4.5 0.4 - - - -
260C THR* 1.3 81.8 + - - +
262C HIS* 1.3 62.5 + - - +
263C LEU* 3.2 12.9 + - - +
264C CYS* 2.8 36.2 + - + +
265C ARG* 2.8 34.2 + - - +
303C PHE* 4.7 2.3 - - - -
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Residues in contact with HIS 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 3.9 21.9 - - + +
106C LEU* 3.4 15.4 - - + +
107C GLN* 3.7 48.3 + - + +
110C TRP* 3.5 26.4 - - + -
111C SER 5.7 0.2 - - - -
260C THR 5.0 6.6 + - - -
261C ASP* 1.3 74.7 + - - +
263C LEU* 1.3 57.4 + - - +
265C ARG* 3.5 22.2 + - - +
266C SER* 2.7 36.4 + - - -
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLU* 3.6 31.0 - - + +
103C LEU* 4.8 10.3 - - + +
106C LEU* 4.0 7.8 - - + +
128C TYR* 3.8 28.3 - - + +
205C ARG* 4.5 16.6 - - - +
261C ASP* 3.2 9.0 + - - +
262C HIS* 1.3 76.9 - - - +
264C CYS* 1.3 60.4 + - - +
266C SER* 3.9 0.7 - - - -
267C ARG* 2.9 55.6 + - + +
303C PHE* 3.7 25.8 - - + -
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Residues in contact with CYS 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C CYS* 2.1 45.3 - - - -
261C ASP* 2.8 28.5 + - + +
263C LEU* 1.3 73.1 - - - +
265C ARG* 1.3 52.5 + - - +
267C ARG* 3.2 3.0 + - - +
268C LEU* 2.6 37.1 + - - +
300C MET* 5.0 3.3 - - - +
303C PHE* 3.5 42.8 - - + -
304C ASP* 4.6 8.1 - - - -
305C MET* 5.2 2.7 - - - -
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Residues in contact with ARG 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C TRP* 3.4 63.0 - - - +
124C GLU* 3.3 36.4 + - - +
258C CYS* 3.4 18.0 + - - +
259C ARG* 3.6 33.3 + - - +
260C THR 5.9 0.4 + - - -
261C ASP 2.8 22.8 + - - +
262C HIS* 3.5 19.0 + - - +
264C CYS* 1.3 72.1 - - - +
266C SER* 1.3 57.2 + - - +
268C LEU* 3.2 7.8 + - + +
269C ALA* 2.7 33.6 + - - +
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Residues in contact with SER 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 3.3 14.8 - - - +
110C TRP* 3.6 20.6 + - - -
125C ALA 4.9 2.0 - - - -
126C SER* 4.8 0.2 - - - -
127C PRO* 4.7 2.7 - - - +
128C TYR* 3.5 26.5 - - - -
262C HIS 2.7 23.5 + - - -
263C LEU 3.9 1.3 - - - -
265C ARG* 1.3 79.9 + - - +
267C ARG* 1.3 50.5 + - - +
269C ALA* 3.1 8.9 + - - +
270C ASP* 2.7 40.4 + - - +
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Residues in contact with ARG 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ARG* 3.8 16.2 - - - +
98C GLY 5.1 2.0 - - - +
102C GLU* 4.1 9.5 + - - -
128C TYR* 3.3 43.4 + - + -
205C ARG* 4.4 10.8 + - - +
209C ASP* 3.3 27.3 + - - -
263C LEU* 2.9 27.8 + - - +
264C CYS* 3.8 4.0 - - - +
266C SER* 1.3 73.2 - - - +
268C LEU* 1.3 60.8 + - - +
270C ASP* 3.2 12.0 + - + +
271C PHE 2.9 23.0 + - - -
296C SER 4.6 1.6 - - - +
299C GLY* 3.0 38.8 + - - +
300C MET* 3.1 19.4 - - - +
301C ILE 4.9 1.4 + - - -
303C PHE* 3.7 24.5 - - + -
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C GLU* 5.8 1.1 - - - +
255C ARG* 3.5 44.4 - - + +
258C CYS* 4.0 20.9 - - + -
259C ARG* 5.5 1.3 - - - +
264C CYS 2.6 21.9 + - - +
265C ARG* 3.3 9.2 - - + +
267C ARG* 1.3 73.3 - - - +
269C ALA* 1.3 61.8 + - - +
271C PHE* 3.2 10.0 + - + +
272C HIS* 3.0 39.0 + - + +
300C MET* 3.5 27.5 - - + -
305C MET* 4.4 18.4 - - + -
342C PHE* 5.4 2.2 - - + -
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Residues in contact with ALA 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C GLU* 3.5 27.1 - - + +
125C ALA 3.1 30.1 - - - +
126C SER* 4.4 1.1 - - - -
255C ARG* 6.3 1.1 - - - +
265C ARG* 2.7 17.6 + - - +
266C SER* 3.1 8.7 + - - +
268C LEU* 1.3 68.8 - - - +
270C ASP* 1.3 54.8 + - - +
272C HIS* 3.1 7.3 + - - +
273C ALA* 2.6 39.3 + - - +
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Residues in contact with ASP 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ARG* 5.6 1.9 - - - +
126C SER* 3.2 21.0 - - - -
128C TYR* 3.3 28.8 - - - +
129C GLU* 3.5 22.1 + - + +
130C PRO* 5.4 0.7 - - - +
266C SER 2.7 27.2 + - - +
267C ARG* 3.2 15.2 + - - +
269C ALA* 1.3 73.2 - - - +
271C PHE* 1.3 61.1 + - - +
273C ALA* 3.1 7.1 + - - +
274C ASN* 3.0 21.3 + - - +
296C SER* 3.2 27.5 + - - +
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Residues in contact with PHE 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ARG 2.9 12.4 + - - +
268C LEU* 3.3 9.0 - - + +
270C ASP* 1.3 75.6 - - - +
272C HIS* 1.3 85.7 + + - +
273C ALA 3.1 0.5 + - - -
275C CYS* 2.6 66.1 + - + +
296C SER* 3.8 9.1 - - - +
297C TYR* 3.9 24.2 - + - -
300C MET* 3.9 18.8 - - + -
341C ASP* 3.6 24.7 - - + -
342C PHE* 3.3 51.4 - + - -
348C LEU* 4.2 3.1 - - + -
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Residues in contact with HIS 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C PHE* 4.1 11.2 - + - +
123C TYR* 3.4 17.8 - - + -
124C GLU 5.9 0.7 - - - +
255C ARG* 3.7 20.6 + - - -
268C LEU* 3.0 36.7 + - + +
269C ALA* 3.1 6.5 + - - +
271C PHE* 1.3 97.6 - + - +
273C ALA* 1.3 50.9 + - - +
276C ARG* 2.8 41.6 + - - +
305C MET* 6.3 0.4 - - - +
338C PHE* 3.5 39.4 - + - +
341C ASP* 2.9 27.8 + - - -
342C PHE* 4.8 2.6 - + - -
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Residues in contact with ALA 273 (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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126C SER* 4.1 15.0 - - - +
129C GLU* 4.2 9.6 - - - +
134C ARG* 5.8 1.1 - - - +
269C ALA 2.6 19.8 + - - +
270C ASP* 3.4 9.9 - - - +
271C PHE 3.1 0.2 - - - -
272C HIS* 1.3 75.2 - - - +
274C ASN* 1.3 63.9 + - - +
276C ARG* 3.7 23.0 + - - +
286C PRO* 3.9 8.5 - - - +
76F TYR* 4.0 15.3 - - - +
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Residues in contact with ASN 274 (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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129C GLU* 2.8 36.1 + - - +
134C ARG* 4.8 6.7 + - - +
270C ASP 3.0 7.0 + - - +
273C ALA* 1.3 77.6 - - - +
275C CYS* 1.3 60.2 + - - +
276C ARG 3.6 1.3 - - - +
285C CYS* 4.6 0.2 - - - -
286C PRO* 3.0 40.3 - - - +
292C ALA* 3.3 36.1 + - + +
293C CYS* 3.5 11.5 - - - +
296C SER* 3.0 23.6 + - - +
347C CYS* 4.3 2.1 - - - -
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Residues in contact with CYS 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C PHE* 2.6 53.3 + - + +
274C ASN* 1.3 70.7 - - - +
276C ARG* 1.3 58.6 + - - +
277C ALA 3.5 0.5 + - - -
293C CYS* 2.1 61.9 - - - -
296C SER* 4.5 2.2 - - - -
297C TYR* 4.0 6.3 - - - -
341C ASP* 3.7 9.2 - - - +
345C ASN* 2.5 30.1 + - - +
347C CYS* 4.9 1.3 - - - -
348C LEU* 4.9 0.2 - - + -
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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