Contacts of the strand formed by residues 35 - 40 (chain A) in PDB entry 2G73
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 PHE 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ALA* 1.3 76.2 - - - +
36A SER* 1.3 69.4 - - - +
37A SER* 4.3 0.2 - - - -
66A VAL* 4.1 13.0 - - + -
67A CYS* 3.4 10.3 - - - +
68A GLY* 2.7 61.5 + - - +
69A HIS 3.7 2.5 - - - -
70A PRO* 4.1 7.2 - - + -
76A ASN* 4.8 3.1 - - - +
79A ALA* 3.4 46.4 - - + -
80A VAL* 3.4 32.3 - - + -
83A ARG* 3.5 19.5 - - + -
118A CYS* 3.6 4.7 - - - -
119A PRO* 3.4 12.8 - - + +
121A PHE* 4.2 14.4 - - + -
186A EIP 3.8 4.3 - - - +
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 1.3 77.1 - - - +
37A SER* 1.3 60.1 + - - +
38A TRP* 4.0 0.3 + - - -
64A ASN* 2.8 22.3 + - - -
66A VAL 3.7 3.8 - - - -
67A CYS* 4.2 7.6 - - - -
118A CYS* 3.7 10.5 - - - -
119A PRO 3.1 6.5 + - - +
120A VAL* 3.2 6.9 - - - -
121A PHE* 2.7 27.7 + - - -
165A GLN* 2.8 42.1 + - - -
186A EIP 4.9 0.7 - - - -
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 4.3 3.8 - - - -
36A SER* 1.3 78.3 + - - +
38A TRP* 1.3 66.4 + - - +
39A LEU* 4.2 9.4 - - - +
64A ASN* 3.0 12.0 - - - +
65A SER* 3.3 2.6 + - - -
66A VAL* 2.8 49.9 + - - -
80A VAL* 3.4 28.0 - - - +
121A PHE* 3.4 15.3 + - - +
122A ALA* 4.2 2.9 + - - -
123A ALA* 5.1 0.5 - - - +
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Residues in contact with TRP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER* 1.3 79.5 - - - +
39A LEU* 1.3 61.1 + - - +
40A PHE* 3.9 3.2 - - + -
46A LEU* 3.6 38.6 - - + -
64A ASN* 3.5 21.9 - - + -
65A SER* 3.6 4.5 - - - -
120A VAL* 3.7 16.8 - - + +
121A PHE 3.0 9.1 + - - +
122A ALA* 3.2 5.4 - - - +
123A ALA 3.1 23.2 + - - +
144A LEU* 4.5 7.9 - - + -
147A VAL* 4.9 2.0 - - + -
148A LEU* 5.6 1.1 - - + -
151A ILE* 4.3 1.6 - - + -
162A MET* 3.9 40.8 - - + -
165A GLN* 2.7 34.0 + - + +
166A ALA* 3.9 18.6 - - + -
175A LEU* 3.5 46.3 - - + +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER* 4.2 9.0 - - - +
38A TRP* 1.3 76.4 - - - +
40A PHE* 1.3 62.6 + - - +
46A LEU* 3.5 3.7 - - - +
47A LEU* 2.8 36.5 + - + +
65A SER* 2.7 25.1 + - - +
66A VAL* 4.0 4.5 - - + -
84A CYS* 3.8 26.0 - - - -
88A LEU* 3.9 24.2 - - + -
90A VAL* 4.4 5.2 - - + -
92A ILE* 4.0 14.6 - - + -
123A ALA* 3.4 28.3 - - + +
125A THR* 4.1 21.3 - - + -
141A TRP* 4.8 0.2 - - - -
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Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TRP 3.9 12.6 - - - -
39A LEU* 1.3 76.3 - - - +
41A ASN* 1.3 66.1 + - - +
44A GLY 3.7 18.8 - - - -
45A GLN 2.9 5.6 - - - +
46A LEU* 3.8 33.2 - - + -
122A ALA* 4.5 0.9 - - + -
123A ALA 3.0 7.8 + - - +
124A ARG* 3.1 10.8 - - - +
125A THR* 3.0 21.9 + - - -
141A TRP* 4.1 3.1 - - - -
144A LEU* 4.3 9.0 - - + -
175A LEU* 3.7 38.8 - - + -
178A PHE* 3.4 55.2 - + + +
179A THR* 4.1 13.5 - - + -
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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