Contacts of the helix formed by residues 281 - 292 (chain B) in PDB entry 4GWO
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 ARG 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B ASP* 4.4 11.1 + - - +
92B LYS 2.4 37.0 + - - +
93B GLY* 5.1 1.2 - - - -
279B PHE* 3.2 35.1 + - - +
280B LEU* 1.3 76.5 - - - +
282B SER* 1.3 71.7 + - - +
283B TYR* 3.3 42.6 + - + +
284B MET* 3.1 32.1 + - + +
285B TYR* 3.3 7.1 + - - -
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 5.1 9.9 - - - -
91B ASP* 4.6 11.1 + - - -
119B TYR* 4.7 4.9 + - - -
280B LEU 3.7 0.6 + - - -
281B ARG* 1.3 78.3 - - - +
283B TYR* 1.3 62.4 + - - +
285B TYR* 3.2 13.9 + - - +
286B ASP* 3.2 21.0 + - - +
297B ARG* 4.0 16.0 + - - +
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Residues in contact with TYR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP* 4.2 14.3 + - + -
92B LYS 4.2 0.4 - - - -
93B GLY* 3.4 8.2 - - - -
94B SER 2.8 46.4 + - - -
95B LEU* 4.1 7.0 - - + -
115B PHE* 3.5 27.2 - + + -
119B TYR* 3.5 37.9 + - + -
122B VAL* 3.5 22.2 - - + -
281B ARG* 3.7 44.8 + - + +
282B SER* 1.3 78.1 + - - +
284B MET* 1.3 87.9 + - + +
286B ASP* 3.5 2.1 - - - +
287B PHE 3.0 22.2 + - - -
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Residues in contact with MET 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B SER 3.8 13.5 - - - +
95B LEU* 4.4 4.3 - - + -
144B ASP* 4.1 18.4 - - - +
145B PHE* 4.0 30.7 - - + -
278B THR* 4.6 5.2 - - + -
279B PHE 3.7 11.2 - - - +
280B LEU* 3.9 10.3 - - + -
281B ARG* 3.1 39.7 + - + +
283B TYR* 1.3 104.1 - - + +
285B TYR* 1.3 57.7 + - - +
287B PHE* 3.0 8.4 + - - +
288B ILE* 2.9 35.2 + - - +
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Residues in contact with TYR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 3.3 50.1 - - + +
281B ARG 3.3 16.5 + - - -
282B SER* 3.2 7.2 + - - +
284B MET* 1.3 76.1 - - - +
286B ASP* 1.3 62.9 + - - +
288B ILE* 3.6 9.2 + - + +
289B GLN* 3.0 26.7 + - - +
295B LEU 4.7 1.4 - - - +
296B THR 5.2 0.4 - - - -
297B ARG* 3.3 78.6 + - + +
300B VAL* 4.0 15.5 - - + -
301B ASP* 2.8 26.1 + - - -
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Residues in contact with ASP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 5.1 4.7 - - - -
115B PHE* 5.7 0.2 - - - -
118B ARG* 4.0 14.3 + - - -
119B TYR* 3.0 29.1 + - + +
282B SER* 3.2 6.9 + - - +
283B TYR 3.5 9.6 - - - +
285B TYR* 1.3 79.0 - - - +
287B PHE* 1.3 56.7 + - - +
289B GLN* 3.4 7.3 + - - +
290B ARG* 2.9 62.6 + - - +
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Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.2 11.4 - - + -
97B ILE* 3.4 31.4 - - + -
108B LEU* 3.9 20.9 - - + -
111B VAL* 3.7 25.1 - - + -
112B ILE* 3.8 13.7 - - + -
115B PHE* 4.0 28.0 - + + -
124B LEU* 5.9 0.2 - - + -
145B PHE* 5.1 7.9 - + + -
147B ILE* 3.9 19.1 - - + -
272B ILE* 4.4 9.2 - - + -
283B TYR 3.0 15.4 + - - +
284B MET* 3.0 9.8 + - - +
286B ASP* 1.3 73.5 - - - +
288B ILE* 1.3 74.2 + - + +
290B ARG* 3.1 8.8 + - - +
291B PHE* 3.0 27.3 + - + +
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Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B PHE* 4.0 27.6 - - + -
161B LEU* 4.8 2.5 - - + -
272B ILE* 4.4 20.4 - - + -
274B PHE* 4.8 8.7 - - + -
280B LEU* 4.9 6.1 - - + -
284B MET 2.9 19.7 + - - +
285B TYR* 3.7 9.0 - - + +
287B PHE* 1.3 81.4 - - + +
289B GLN* 1.3 58.7 + - - +
291B PHE* 3.3 5.9 + - - +
292B ALA* 2.9 28.2 + - - +
295B LEU* 3.6 36.6 - - + +
300B VAL* 4.0 23.6 - - + -
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Residues in contact with GLN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B TYR 3.0 19.3 + - - +
286B ASP* 3.9 7.6 - - - +
288B ILE* 1.3 72.7 - - - +
290B ARG* 1.3 69.5 + - - +
291B PHE 3.2 1.3 - - - -
292B ALA 3.5 7.0 - - - -
293B PRO* 2.7 49.9 + - - +
295B LEU 3.7 11.4 - - - +
296B THR* 3.6 18.3 - - - +
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 3.8 31.9 - - + +
114B GLY* 3.4 35.7 + - - -
115B PHE* 4.6 10.9 - - + +
118B ARG* 3.9 36.1 - - - +
119B TYR* 4.6 2.0 - - - -
286B ASP* 2.9 53.6 + - - +
287B PHE* 3.3 7.4 - - - +
289B GLN* 1.3 83.3 - - - +
291B PHE* 1.3 58.4 + - - +
293B PRO* 4.7 5.0 - - - +
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Residues in contact with PHE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLN* 3.8 21.1 - - - -
107B ALA* 3.6 20.2 - - + -
108B LEU* 3.6 30.1 - - + -
111B VAL* 4.1 18.2 - - + -
147B ILE* 3.6 32.5 - - + -
163B CYS* 3.8 36.2 - - + +
164B TYR* 3.9 14.8 - + - -
270B THR* 4.6 0.4 - - + -
272B ILE* 5.2 3.6 - - + -
287B PHE* 3.0 20.6 + - + +
288B ILE* 3.7 5.4 - - - +
290B ARG* 1.3 78.3 - - - +
292B ALA* 1.3 60.4 + - - +
293B PRO* 3.9 4.7 - - - +
322B PRO* 5.9 0.5 - - - +
324B LYS* 4.3 13.5 + - - -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B CYS* 3.8 20.0 - - + +
288B ILE 2.9 11.4 + - - +
289B GLN* 3.3 4.4 - - - +
291B PHE* 1.3 78.6 - - - +
293B PRO* 1.3 59.0 - - - +
294B HIS* 3.2 25.8 - - + -
295B LEU* 2.7 51.4 + - + +
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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
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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