Contacts of the strand formed by residues 35 - 39 (chain B) in PDB entry 6Y2G
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 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU 3.4 2.6 - - - +
31B TRP* 3.5 1.2 - - - -
32B LEU 3.0 31.4 + - - +
33B ASP* 3.5 1.2 + - + -
34B ASP* 1.3 92.9 - - - +
36B VAL* 1.4 74.4 + - - +
37B TYR* 3.5 38.2 - - + +
88B LYS* 3.9 21.8 - - + -
89B LEU 3.5 6.5 - - - +
90B LYS* 4.2 16.8 - - + +
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 3.9 20.2 - - + -
20B VAL* 4.0 20.2 - - + -
29B GLY* 4.0 8.7 - - - -
30B LEU 3.2 4.5 - - - +
31B TRP* 4.0 24.7 - - + -
35B VAL* 1.4 75.9 - - - +
37B TYR* 1.3 63.9 + - - +
38B CYS* 5.0 0.7 - - + -
68B VAL* 4.0 21.5 - - + -
75B LEU* 4.6 1.1 - - + -
87B LEU 3.6 1.6 - - - +
88B LYS* 3.5 2.8 - - - -
89B LEU* 2.8 46.4 + - + +
91B VAL* 4.1 14.4 - - + -
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Residues in contact with TYR 37 (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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29B GLY* 3.2 4.0 - - - -
30B LEU* 2.7 51.5 + - + +
32B LEU* 4.3 17.3 + - + -
35B VAL* 3.5 34.3 - - + +
36B VAL* 1.3 70.8 - - - +
38B CYS* 1.3 60.7 + - - +
83B GLN* 5.8 0.4 - - - -
86B VAL* 4.4 12.6 - - + -
87B LEU 3.5 5.4 - - - +
88B LYS* 3.5 35.5 - - + +
101B TYR* 4.3 9.7 + - - -
103B PHE* 3.8 39.1 - + - -
162B MET* 3.5 8.6 - - + +
177B LEU* 4.3 20.9 - - + -
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Residues in contact with CYS 38 (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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20B VAL* 4.4 18.2 - - + -
27B LEU* 4.3 4.3 - - + -
28B ASN 3.6 13.0 - - - +
29B GLY* 4.1 4.7 - - - -
36B VAL* 5.0 0.9 - - + -
37B TYR* 1.3 76.9 - - - +
39B PRO* 1.3 81.3 - - + +
42B VAL* 3.9 17.3 - - - -
86B VAL* 3.5 5.2 - - - +
87B LEU* 2.9 47.5 + - - -
89B LEU* 4.7 6.7 - - - -
162B MET* 3.7 10.5 - - - +
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Residues in contact with PRO 39 (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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27B LEU* 4.1 12.8 - - + -
28B ASN 4.0 2.5 - - - +
38B CYS* 1.3 90.8 - - + +
40B ARG* 1.3 66.4 + - - +
41B HIS* 3.0 23.1 + - + +
42B VAL* 3.3 23.0 + - - +
85B CYS 3.9 5.4 - - - +
145B CYS 4.5 0.2 - - - -
146B GLY* 3.8 27.8 - - - +
162B MET* 3.7 16.6 - - + -
163B HIS 3.9 9.9 - - - +
164B HIS* 3.6 18.4 - - + -
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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
------------------------------------------------------------
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