Contacts of the strand formed by residues 304 - 309 (chain W) 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 LEU 304 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W ALA* 4.6 25.8 - - + +
34W ARG* 4.2 16.8 - - - +
50W PRO* 4.4 15.0 - - + -
51W LYS 4.2 17.3 - - - +
52W ASN* 3.8 9.4 - - - +
53W ILE* 5.3 0.9 - - + +
70W LEU* 5.3 2.5 - - + -
252W GLY 2.8 16.5 + - - +
253W ILE* 3.2 17.3 - - + -
254W VAL* 2.7 32.4 + - - +
303W ILE* 1.3 78.0 - - - +
305W PHE* 1.3 57.6 + - - +
306W ILE* 3.5 34.3 - - + -
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Residues in contact with PHE 305 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52W ASN* 2.5 37.4 + - + +
53W ILE 3.0 26.4 + - - +
99W ILE* 5.8 0.2 - - + -
100W ILE* 5.6 1.6 - - + -
254W VAL* 3.3 46.9 - - + -
256W ILE* 5.0 13.5 - - + -
285W LEU* 3.1 47.1 - - + -
286W VAL* 3.4 31.6 - - + -
300W THR 5.2 1.8 - - - -
303W ILE* 4.3 25.1 - - + -
304W LEU* 1.3 74.9 - - - +
306W ILE* 1.3 66.7 + - - +
307W ALA* 4.2 0.7 - - + -
327W LEU* 5.0 4.9 - - + -
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Residues in contact with ILE 306 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27W VAL* 5.0 6.7 - - + -
53W ILE* 3.2 22.9 - - + +
55W MET* 3.1 39.3 - - + -
67W ALA* 4.2 15.5 - - + -
70W LEU* 4.2 21.5 - - + -
253W ILE* 4.4 6.7 - - + -
254W VAL 2.7 11.3 + - - +
255W PHE* 3.0 20.5 - - + -
256W ILE* 2.9 22.8 + - - -
304W LEU* 3.5 22.7 - - + -
305W PHE* 1.3 79.6 - - - +
307W ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 307 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53W ILE 2.9 9.1 + - - -
54W LEU* 3.2 26.9 - - + +
55W MET* 2.7 33.3 + - - +
256W ILE* 3.3 20.9 - - + +
259W ILE* 4.1 24.2 - - + -
305W PHE* 4.2 1.1 - - + -
306W ILE* 1.3 74.0 - - - +
308W SER* 1.3 55.6 + - - +
327W LEU* 5.2 2.9 - - + -
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Residues in contact with SER 308 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55W MET* 3.6 7.0 - - - -
63W LYS* 2.9 27.8 + - - -
255W PHE* 3.8 19.3 - - - -
256W ILE 2.9 7.0 + - - +
257W ASP* 2.5 39.0 + - - -
258W GLU 3.0 2.6 + - - -
259W ILE* 3.0 27.0 + - - +
306W ILE 4.1 1.2 + - - -
307W ALA* 1.3 75.0 - - - +
309W GLY* 1.3 57.4 + - - +
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Residues in contact with GLY 309 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55W MET 2.9 11.4 + - - +
56W ILE* 3.5 3.8 - - - -
57W GLY 3.1 26.2 + - - -
63W LYS* 4.0 4.0 - - - +
258W GLU* 4.6 2.9 - - - -
259W ILE* 4.6 0.2 - - - -
260W ASP* 3.0 15.7 - - - -
308W SER* 1.3 77.8 - - - +
310W ALA* 1.3 64.5 + - - -
311W PHE* 3.3 13.2 + - - +
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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
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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