Contacts of the strand formed by residues 38 - 44 (chain B) in PDB entry 2C2V
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 TYR 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B PRO* 3.4 3.1 - - - +
32B ASP* 2.7 38.4 + - + -
35B ASN* 3.3 23.7 + - + +
36B ALA 3.6 0.2 - - - -
37B ARG* 1.3 77.9 - - - +
39B PHE* 1.3 66.8 + - - +
40B HIS* 2.9 48.2 + + - -
59B GLU* 2.6 45.3 + - + +
60B LEU 3.6 8.1 - - - -
61B PHE* 4.4 4.7 - - + +
76B MET* 4.5 6.1 - - - +
39C PRO* 3.3 37.7 - - + -
41C ASN* 4.8 1.4 + - + -
42C PHE* 4.3 2.7 - + - -
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 5.1 0.9 - - + -
16B THR* 3.9 32.3 - - + -
19B LEU* 5.0 10.1 - - + -
20B LEU* 6.5 0.4 - - + -
29B ALA* 4.8 6.3 - - + -
30B GLU 3.6 11.2 - - - +
31B PRO* 4.0 23.6 - - + -
36B ALA 3.4 22.9 - - - -
37B ARG 3.6 7.0 - - - -
38B TYR* 1.3 86.1 - - - +
40B HIS* 1.3 61.6 + - - +
41B VAL* 3.4 6.2 + - + -
59B GLU* 3.8 6.1 - - - +
60B LEU* 2.7 51.3 + - + -
62B LEU* 3.9 22.0 - - + -
105B ILE* 4.2 18.6 - - + -
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Residues in contact with HIS 40 (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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28B LYS* 3.5 18.9 + - - +
29B ALA* 3.2 19.3 - - - -
30B GLU* 3.0 17.7 + - + +
31B PRO 4.4 0.7 - - - -
32B ASP* 2.3 49.1 + - - -
38B TYR* 2.9 34.0 + + - -
39B PHE* 1.3 71.3 - - - +
41B VAL* 1.4 60.6 - - - +
42B VAL* 5.6 0.2 - - - -
58B LEU 4.6 1.6 - - - -
59B GLU* 5.1 1.3 - - - +
76B MET* 5.7 4.8 - - - +
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Residues in contact with VAL 41 (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 ILE* 4.1 14.8 - - + -
28B LYS 3.8 8.7 - - - +
29B ALA* 4.0 12.3 - - + -
39B PHE* 3.4 11.6 + - + +
40B HIS* 1.4 76.5 - - - +
42B VAL* 1.3 74.4 + - - +
43B ILE* 4.3 4.0 - - + -
57B LYS* 3.5 1.0 - - - -
58B LEU* 2.8 53.8 + - + +
59B GLU* 4.5 0.7 - - - -
60B LEU* 4.0 24.2 - - + +
73B VAL* 6.1 0.7 - - + -
76B MET* 5.6 0.2 - - - +
109B LEU* 4.5 15.7 - - + -
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Residues in contact with VAL 42 (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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26B GLY 4.3 0.2 - - - +
27B ILE* 3.2 4.7 - - - -
28B LYS* 2.9 61.9 + - + +
40B HIS 4.1 0.2 + - - -
41B VAL* 1.3 79.2 - - - +
43B ILE* 1.4 67.6 + - - +
44B ALA* 4.0 1.5 + - + +
55B THR* 4.6 15.0 - - + -
56B PHE 3.3 12.8 - - - +
57B LYS* 4.4 17.0 - - + -
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Residues in contact with ILE 43 (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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26B GLY 4.1 6.3 - - - +
27B ILE* 4.3 19.1 - - + +
41B VAL* 4.3 9.6 - - + -
42B VAL* 1.4 75.2 - - - +
44B ALA* 1.3 71.0 + - - +
55B THR* 3.7 0.5 - - - -
56B PHE* 2.7 35.6 + - + +
58B LEU* 3.7 28.3 - - + -
75B PHE* 5.2 1.8 - - + -
109B LEU* 4.8 6.1 - - + +
112B ILE* 3.5 33.4 - - + -
113B GLN* 4.1 22.0 - - + +
116B LEU* 5.1 9.9 - - + -
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Residues in contact with ALA 44 (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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26B GLY* 3.1 25.9 + - - +
42B VAL* 4.0 2.0 + - + -
43B ILE* 1.3 85.7 - - - +
45B GLY* 1.3 65.0 + - - +
46B PRO* 3.0 10.9 - - - +
54B GLY 3.8 8.1 - - - +
55B THR* 4.2 11.4 - - + +
56B PHE* 4.6 0.7 - - - -
113B GLN* 4.7 4.2 - - - +
116B LEU* 4.9 0.3 - - - +
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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