Contacts of the strand formed by residues 34 - 41 (chain A) in PDB entry 3VTU
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 LYS 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 4.8 2.6 - - + +
28A ARG* 3.0 20.6 + - - -
31A HIS* 2.9 24.6 + - + +
33A THR* 1.3 84.5 + - - +
35A ILE* 1.4 64.8 + - - +
36A PRO* 3.7 3.8 - - - +
57A LEU* 3.8 40.2 - - + +
58A VAL 3.4 1.1 - - - +
59A PRO* 3.6 35.6 - - + +
202A SO4 2.8 47.0 + - - +
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.9 18.6 - - - +
34A LYS* 1.4 75.8 - - - +
36A PRO* 1.3 66.4 - - - +
37A VAL* 3.4 21.3 + - + +
56A PHE 3.3 5.0 - - - +
57A LEU* 3.6 2.2 - - - -
58A VAL 2.7 36.3 + - - +
60A ASP* 4.0 17.5 - - + -
99A ILE* 3.9 33.9 - - + +
100A SER* 4.2 7.9 - - - -
103A TYR* 3.5 45.5 - - + -
113A LEU* 4.5 1.8 - - + -
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Residues in contact with PRO 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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24A VAL* 4.3 11.9 - - + -
27A ILE* 4.0 22.0 - - + -
28A ARG* 4.1 9.9 - - - +
34A LYS 3.7 7.6 - - - +
35A ILE* 1.3 86.2 - - + +
37A VAL* 1.3 62.3 + - - +
55A LYS* 5.9 0.2 - - + -
56A PHE 3.7 4.7 - - - +
57A LEU* 4.6 4.3 - - + -
103A TYR* 3.8 14.8 - - + +
111A GLY 3.6 20.0 - - - +
112A PHE* 3.6 24.9 - - + -
113A LEU* 3.0 24.8 + - - +
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Residues in contact with VAL 37 (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 ILE* 3.5 29.2 - - + +
36A PRO* 1.3 78.8 - - - +
38A ILE* 1.3 64.7 + - - +
39A ILE* 3.6 24.9 - - + -
54A THR 3.5 0.9 - - - +
55A LYS* 3.4 3.7 - - - +
56A PHE* 2.7 43.0 + - + +
58A VAL* 3.8 11.4 - - + -
67A LEU* 5.3 0.2 - - + -
99A ILE* 3.7 18.8 - - + -
112A PHE* 4.3 0.8 - - - -
113A LEU* 3.2 14.1 - - + +
115A MET* 3.8 24.0 - - + -
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Residues in contact with ILE 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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11A PHE* 3.5 40.2 - - + -
37A VAL* 1.3 72.4 - - - +
39A ILE* 1.3 63.9 + - - +
40A GLU* 3.8 17.3 - - - +
54A THR* 3.4 18.2 - - + +
55A LYS* 3.8 20.2 - - + -
112A PHE* 3.7 38.4 - - + -
113A LEU 2.8 7.9 + - - +
114A TYR* 3.7 26.7 - - + -
115A MET 2.8 28.2 + - - +
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Residues in contact with ILE 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 VAL* 3.6 20.6 - - + -
38A ILE* 1.3 78.1 - - - +
40A GLU* 1.3 69.2 + - - +
51A LEU* 3.7 26.7 - - + +
53A LYS 4.0 0.7 - - - +
54A THR* 3.0 19.5 + - - +
56A PHE* 3.7 29.8 - - + -
67A LEU* 4.4 12.3 - - + -
71A ILE* 3.5 32.8 - - + -
85A LEU* 4.4 16.2 - - + -
115A MET* 3.5 14.1 - - + +
117A TYR* 4.0 15.5 - - + -
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Residues in contact with GLU 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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9A LYS 5.0 0.2 - - - +
10A THR* 3.6 16.3 - - - -
11A PHE* 2.8 33.5 + - - +
12A LYS 5.3 0.3 + - - -
14A ARG* 4.4 3.3 + - - -
38A ILE* 3.8 22.9 - - + +
39A ILE* 1.3 82.4 - - - +
41A ARG* 1.3 67.8 + - - +
51A LEU* 5.8 0.4 - - - -
54A THR* 4.0 9.1 - - + +
114A TYR* 4.3 9.7 - - - -
115A MET 3.0 10.4 + - - +
116A VAL* 3.1 14.6 - - + +
117A TYR* 2.9 28.4 + - - -
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Residues in contact with ARG 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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8A GLU* 3.0 36.7 + - - +
40A GLU* 1.3 77.6 - - - +
42A TYR* 1.4 73.4 + - - +
43A LYS* 3.4 3.8 + - - -
45A GLU* 3.5 34.2 + - + +
48A LEU 2.9 29.5 + - - -
49A PRO* 3.8 9.0 - - - +
50A VAL* 3.4 34.4 - - + +
51A LEU* 5.7 0.8 - - - +
116A VAL* 4.2 1.1 - - - +
117A TYR* 3.4 32.5 - - + +
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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