Contacts of the strand formed by residues 35 - 40 (chain F) 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 ALA 35 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ARG* 2.8 30.8 + - - +
34F ASP* 1.3 90.4 + - - +
36F TYR* 1.3 59.9 + - - +
37F TRP* 3.3 12.9 - - + -
143F ALA* 4.2 0.4 - - - +
144F ARG 3.1 13.0 - - - +
146F TYR* 3.8 20.0 - - + -
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Residues in contact with TYR 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F PHE* 4.9 0.4 - + - -
32F SER* 2.8 22.7 + - - -
33F ARG* 3.4 50.5 + - + +
35F ALA* 1.3 75.1 - - - +
37F TRP* 1.3 68.3 + - - +
51F LEU* 4.1 9.6 - - + -
52F TYR 3.2 26.0 - - - -
53F VAL* 3.7 28.0 - - + -
54F HIS* 3.1 22.7 + + - -
143F ALA* 4.0 12.3 - - + -
144F ARG 3.2 5.1 + - - -
145F VAL* 3.8 20.6 - - + -
146F TYR* 2.5 34.9 + - - +
186F HIS* 5.3 2.2 - + - -
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Residues in contact with TRP 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F ARG* 4.2 10.5 - - - -
35F ALA* 3.3 22.9 - - + -
36F TYR* 1.3 93.1 - - - +
38F GLU* 1.3 69.1 + - - +
51F LEU* 3.3 14.3 - - - +
146F TYR* 3.1 23.6 - - + +
147F PHE* 4.4 0.9 - - - +
148F SER* 5.5 1.3 - - - +
168F PRO* 3.1 29.8 - - + +
169F GLU* 3.9 21.8 - - + +
170F THR* 2.8 49.0 + - + +
171F ARG 3.4 18.6 - - - -
172F PRO* 3.9 10.5 - - + -
173F SER* 4.4 6.5 - - - -
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Residues in contact with GLU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F TRP* 1.3 84.1 - - - +
39F LYS* 1.3 98.4 + - - +
40F LEU 3.6 0.7 + - - -
50F LEU* 4.0 15.3 - - + +
51F LEU* 3.9 7.0 - - + +
146F TYR 3.8 0.6 + - - -
147F PHE* 3.5 30.5 - - + -
148F SER* 3.0 25.6 + - - -
168F PRO* 6.2 0.4 - - - -
169F GLU* 4.9 7.7 + - - -
190F LEU* 3.6 29.0 - - - +
192F PRO* 3.4 35.2 - - + +
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Residues in contact with LYS 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F GLU* 1.3 94.3 + - - +
40F LEU* 1.3 65.8 + - - +
41F TYR* 3.4 38.4 + - + +
44F GLN* 4.3 4.7 + - - -
50F LEU* 5.3 0.5 - - - +
148F SER* 3.3 9.6 - - - +
150F PHE* 3.7 19.9 - - + -
164F GLU* 2.8 42.5 + - + +
169F GLU* 3.4 49.3 - - + +
192F PRO* 5.2 4.9 - - - +
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Residues in contact with LEU 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F GLU 5.3 0.2 - - - -
39F LYS* 1.3 76.1 - - - +
41F TYR* 1.3 68.8 + - - +
44F GLN* 3.2 11.7 - - - +
50F LEU* 3.4 38.8 - - + -
86F ILE* 4.8 8.5 - - + -
97F LEU* 4.3 7.0 - - + -
101F LEU* 4.1 18.8 - - + -
121F VAL* 4.7 9.6 - - + -
147F PHE* 3.4 37.5 - - + -
148F SER 2.7 17.6 + - - +
149F PHE* 3.2 16.2 - - + -
150F PHE* 3.2 24.9 + - - -
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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