Contacts of the strand formed by residues 39 - 42 (chain A) in PDB entry 2G1O
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 VAL 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.9 6.3 - - + -
21A ILE* 5.5 0.4 - - + -
37A SER 5.5 0.7 - - - +
38A ASN* 1.3 81.7 - - - +
40A TRP* 1.3 68.2 + - - +
41A VAL* 5.2 2.7 - - + -
74A LEU* 5.5 0.5 - - - +
76A LEU* 5.3 0.3 - - - +
92A ILE* 4.1 15.7 - - + -
101A GLN* 4.4 13.2 + - + +
102A MET 4.6 3.8 + - - +
103A PHE* 3.3 22.2 - - + +
104A GLY 2.8 23.9 + - - -
122A VAL 3.1 8.1 - - - +
123A VAL* 4.0 31.9 - - + -
124A GLY 4.2 2.2 - - - +
135A VAL* 6.4 0.2 - - - +
138A ILE* 4.1 22.7 - - + +
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Residues in contact with TRP 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 ASN 4.9 2.2 - - - -
39A VAL* 1.3 79.0 - - - +
41A VAL* 1.3 73.9 + - - +
42A PRO* 4.0 11.0 - - + -
76A LEU* 3.3 23.6 - - + -
78A TYR* 2.8 31.6 + + - -
83A VAL* 3.8 24.7 - - + -
103A PHE* 4.7 0.9 - - - -
104A GLY 3.3 15.9 - - - +
106A VAL* 3.3 29.2 - - + -
109A MET* 4.1 9.4 - - + -
114A PHE* 4.0 20.9 - + - -
119A PHE* 5.0 1.8 - + - -
120A ASP 3.4 25.6 - - - -
121A GLY* 3.2 3.4 - - - -
122A VAL* 2.8 69.4 + - + +
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Residues in contact with VAL 41 (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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19A ILE* 4.6 2.5 - - + -
21A ILE* 3.6 31.2 - - + -
28A PHE* 3.8 26.7 - - + -
30A VAL* 4.4 10.5 - - + -
39A VAL* 5.2 2.7 - - + -
40A TRP* 1.3 85.7 - - - +
42A PRO* 1.3 75.1 - - + +
43A SER 3.5 0.2 + - - -
59A PHE* 3.8 28.3 - - + -
103A PHE* 4.5 11.9 - - + -
104A GLY 3.3 3.3 + - - +
105A GLU* 3.7 2.5 - - - -
106A VAL 3.2 17.7 + - - -
121A GLY* 4.3 1.1 - - - -
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Residues in contact with PRO 42 (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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40A TRP* 4.0 1.8 - - + -
41A VAL* 1.3 90.4 - - + +
43A SER* 1.3 59.3 + - - +
53A CYS* 4.8 1.6 - - - -
56A HIS* 4.2 6.1 - - + -
57A LYS 3.2 21.3 - - - +
58A LEU* 3.3 16.6 - - + -
59A PHE* 2.8 26.7 + - - +
106A VAL* 4.1 10.3 - - + +
109A MET* 3.7 28.0 - - + -
120A ASP* 3.0 34.1 - - + +
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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