Contacts of the helix formed by residues 274 - 288 (chain B) in PDB entry 1G3I
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 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE 5.0 0.3 - - - +
87B THR* 4.1 23.2 - - - +
271B ALA* 3.4 28.4 + - - -
273B VAL* 1.3 84.4 - - - +
275B ARG* 1.3 58.4 + - - +
277B GLY* 3.9 3.5 + - - -
278B VAL* 3.9 15.1 + - - +
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Residues in contact with ARG 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 5.8 3.4 - - - -
87B THR* 3.8 22.9 - - + +
261B LYS 3.5 19.3 + - - +
262B ILE* 3.5 25.8 - - + +
263B CYS 4.0 11.6 + - - +
265B LYS* 3.7 38.6 - - - +
271B ALA 4.2 8.3 + - - +
272B ASP* 2.9 38.0 + - - +
274B SER* 1.3 76.5 - - - +
276B GLU* 1.3 53.5 + - - +
277B GLY 2.5 16.0 + - - -
278B VAL* 2.8 23.4 + - - +
279B GLN 3.7 1.4 + - - -
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE 4.2 0.6 + - - -
263B CYS 4.9 0.4 + - - -
264B LYS* 2.9 41.8 - - + +
272B ASP* 2.8 25.5 + - - +
273B VAL* 4.0 14.7 - - - +
275B ARG* 1.3 71.2 - - - +
277B GLY* 1.3 57.6 + - - +
279B GLN* 4.0 16.9 - - - +
280B ARG* 3.8 37.7 + - - +
320B ILE* 4.0 15.3 - - + +
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Residues in contact with GLY 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL 3.4 14.4 + - - -
274B SER 4.2 3.1 - - - -
275B ARG 2.5 9.3 + - - -
276B GLU* 1.3 74.3 - - - +
278B VAL* 1.3 62.6 + - - -
279B GLN 2.7 6.2 + - - -
280B ARG* 2.8 20.3 + - - +
281B ASP* 2.8 20.4 + - - +
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA 3.6 21.3 - - - +
86B PHE* 3.3 46.0 - - + +
87B THR* 4.2 6.1 - - - +
96B VAL* 4.9 0.7 - - + -
262B ILE* 3.8 19.3 - - + -
274B SER 3.9 11.6 + - - +
275B ARG* 2.8 13.4 + - - +
277B GLY* 1.3 76.6 - - - +
279B GLN* 1.3 61.3 + - - +
281B ASP* 3.2 12.6 + - + +
282B LEU* 2.9 28.8 + - + +
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Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ILE* 5.8 0.2 - - + -
262B ILE* 2.8 38.1 + - + +
263B CYS* 3.8 2.0 - - - +
264B LYS* 2.4 33.8 - - - +
275B ARG 4.2 1.1 - - - +
276B GLU* 4.0 9.5 - - - +
277B GLY 2.7 1.8 + - - -
278B VAL* 1.3 77.5 - - - +
280B ARG* 1.3 57.6 + - - +
282B LEU* 2.9 21.7 + - - +
283B LEU* 3.0 14.4 + - - +
319B LEU* 3.3 16.7 - - + +
320B ILE* 2.9 44.8 + - + +
323B LEU* 3.5 18.2 - - + +
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Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 2.9 41.4 - - + +
84A THR* 4.2 25.1 + - - +
85A LYS* 6.5 0.9 - - - -
258A GLU* 3.6 13.6 + - - -
261A LYS* 4.1 26.6 - - - +
276B GLU* 3.8 38.6 + - - +
277B GLY* 2.8 13.1 + - - +
279B GLN* 1.3 72.4 - - - +
281B ASP* 1.3 61.4 + - - +
283B LEU* 3.5 10.2 - - - +
284B PRO* 3.4 18.0 - - - +
320B ILE* 4.0 25.8 - - + +
322B GLU* 5.3 4.0 + - - -
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Residues in contact with ASP 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LYS* 4.9 17.1 - - - +
86B PHE* 5.7 1.2 - - + +
96B VAL* 3.5 32.8 - - + +
277B GLY* 2.8 28.3 + - - +
278B VAL* 3.4 14.0 + - + +
279B GLN 3.0 0.2 - - - -
280B ARG* 1.3 80.6 - - - +
282B LEU* 1.3 59.5 + - - +
284B PRO* 3.4 13.3 - - - +
285B LEU* 4.7 0.5 - - - +
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 6.2 0.2 - - + -
83B ALA* 5.7 1.6 - - + -
86B PHE* 5.2 3.1 - - + -
96B VAL* 3.4 27.8 - - + -
99B ILE* 3.8 18.8 - - + -
256B ILE* 3.6 31.4 - - + -
259B ILE* 4.3 17.7 - - + -
262B ILE* 4.4 12.1 - - + -
278B VAL* 2.9 19.2 + - + +
279B GLN* 2.9 9.7 + - - +
281B ASP* 1.3 76.7 - - - +
283B LEU* 1.3 68.8 + - - +
284B PRO 3.3 0.2 - - - -
285B LEU* 2.9 24.2 + - + +
286B VAL* 3.2 17.3 + - + +
305B PHE* 6.3 0.2 - - + -
323B LEU* 5.4 8.1 - - + -
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 4.4 18.6 - - - +
279B GLN 3.0 11.4 + - - +
280B ARG* 3.5 13.5 - - - +
282B LEU* 1.3 74.5 - - - +
284B PRO* 1.3 64.4 - - + +
285B LEU 3.0 1.0 + - - -
286B VAL* 3.1 3.1 + - + -
287B GLU* 2.4 64.5 + - + +
320B ILE* 3.8 15.5 - - + -
322B GLU* 3.4 47.1 - - + +
323B LEU* 4.0 15.7 - - + +
326B ARG* 5.1 2.7 - - + -
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Residues in contact with PRO 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 5.8 5.6 - - + +
85A LYS* 6.5 0.9 - - + -
97B ASP* 6.0 0.9 - - - +
280B ARG 3.4 12.3 - - - +
281B ASP* 3.4 9.0 - - - +
282B LEU 3.4 4.3 - - - -
283B LEU* 1.3 99.1 - - + +
285B LEU* 1.3 62.6 + - + +
287B GLU* 4.3 5.4 - - + +
288B GLY 2.8 24.2 + - - +
289B SER* 2.9 28.7 + - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.9 37.7 - - + +
97B ASP* 4.0 14.6 - - - +
99B ILE* 4.1 18.8 - - + -
100B ILE* 3.6 35.9 - - + -
281B ASP 4.7 0.2 - - - +
282B LEU* 2.9 16.0 + - + +
284B PRO* 1.3 78.7 - - + +
286B VAL* 1.3 73.0 + - + +
288B GLY* 3.0 3.1 + - - -
289B SER* 4.4 6.7 - - - +
291B VAL* 4.7 1.1 - - + -
300B THR* 2.9 32.4 + - + +
305B PHE* 3.8 17.6 - - + -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 4.2 7.7 + - - +
256B ILE* 5.2 5.8 - - + -
282B LEU* 3.2 12.5 + - + +
283B LEU* 3.1 7.6 + - + +
285B LEU* 1.3 83.0 - - + +
287B GLU* 1.3 63.0 + - + +
288B GLY* 3.2 0.9 + - - -
300B THR 4.5 3.3 - - - +
301B ASP 5.1 3.1 - - - +
305B PHE* 3.5 40.3 - - + -
323B LEU* 4.2 22.7 - - + -
326B ARG* 3.3 52.2 + - + +
327B LEU* 5.2 4.5 - - + -
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 4.2 15.5 + - - +
80A LYS* 3.2 31.9 + - - -
82A GLU* 5.7 0.3 - - - +
394A ARG* 5.0 5.3 + - - +
450A ATP 6.1 0.9 - - - -
283B LEU* 2.4 57.7 + - + +
284B PRO* 4.3 3.5 - - + +
286B VAL* 1.3 72.2 - - - +
288B GLY* 1.3 60.3 + - - +
301B ASP* 5.1 1.4 - - - +
322B GLU* 4.3 11.4 - - - +
326B ARG* 3.8 34.3 + - + +
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 4.4 16.8 + - - -
284B PRO* 2.8 11.3 + - - +
285B LEU 3.0 4.7 + - - -
286B VAL 3.2 0.4 - - - -
287B GLU* 1.3 83.5 - - - +
289B SER* 1.3 60.5 + - - -
300B THR* 3.4 7.6 - - - -
301B ASP* 3.8 28.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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