Contacts of the strand formed by residues 32 - 41 (chain A) in PDB entry 5V35
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 ARG 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLY 3.6 2.0 + - - +
31A SER* 1.3 73.0 - - - +
33A VAL* 1.3 61.7 + - - +
34A ILE* 4.1 8.2 + - + +
60A HIS* 5.9 4.7 - - + -
61A ILE 3.1 10.5 - - - +
62A ILE* 3.8 17.5 - - + -
155A GLN 4.1 0.3 - - - +
156A VAL* 3.6 3.6 - - - +
157A ASP* 2.9 44.5 + - + +
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 4.3 22.7 - - + -
31A SER 4.6 0.4 - - - +
32A ARG* 1.3 74.4 - - - +
34A ILE* 1.3 58.9 + - - +
35A PHE* 3.5 8.0 - - + -
60A HIS* 3.5 3.3 - - - -
61A ILE* 2.8 44.9 + - + -
63A ILE* 3.7 34.1 - - + -
76A LEU* 4.3 19.3 - - + -
153A LEU* 3.3 31.2 - - + -
155A GLN 3.8 3.6 - - - +
156A VAL* 4.5 5.6 - - + +
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Residues in contact with ILE 34 (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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32A ARG* 4.7 8.7 - - + +
33A VAL* 1.3 77.2 - - - +
35A PHE* 1.3 64.3 + - - +
58A PRO* 4.4 6.1 - - + -
59A MET 3.2 7.9 - - - +
60A HIS* 3.8 34.8 - - + +
153A LEU* 3.6 2.6 - - - +
154A LEU* 2.8 44.7 + - + -
155A GLN* 2.9 50.0 + - + +
157A ASP* 3.7 9.6 - - - +
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Residues in contact with PHE 35 (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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33A VAL* 3.5 22.0 - - + -
34A ILE* 1.3 76.6 - - - +
36A HIS* 1.3 68.6 + - - +
37A PHE* 4.1 17.3 - + + -
58A PRO* 3.4 7.1 - - - +
59A MET* 2.8 69.3 + - + +
61A ILE* 4.0 15.5 - - + -
76A LEU* 3.9 33.2 - - + -
151A ILE* 3.9 14.1 - - + -
152A GLU 3.2 18.8 - - - +
153A LEU* 4.1 5.4 - - + -
154A LEU* 4.0 4.7 - - - -
201A FAR 4.1 24.0 - - + -
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Residues in contact with HIS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 1.3 75.5 - - - +
37A PHE* 1.3 61.9 + - - +
52A SER* 2.7 35.1 + - - +
53A ARG* 3.6 53.9 + - + +
56A GLY 4.3 5.2 + - - -
57A GLN 3.8 6.1 - - - -
58A PRO* 3.5 36.8 - - + +
151A ILE* 3.1 7.1 - - - +
152A GLU* 2.9 36.2 + - + +
154A LEU* 4.2 20.1 - - + +
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Residues in contact with PHE 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 PHE* 4.1 19.5 - + + -
36A HIS* 1.3 76.4 - - - +
38A ARG* 1.3 62.1 + - - +
39A THR* 3.3 26.9 - - - -
50A ASP* 3.9 18.4 - - + -
51A ASP* 3.5 4.2 - - - +
52A SER* 2.9 52.4 + - - -
59A MET* 4.3 22.9 - - + -
97A TYR* 3.6 10.8 - - - -
104A LEU* 3.9 23.8 - - + -
149A PHE* 5.7 0.4 - - + -
150A VAL 3.2 9.6 - - - +
151A ILE* 4.1 13.5 - - + -
201A FAR 3.3 22.0 - - + -
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Residues in contact with ARG 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 PHE* 1.3 76.8 - - - +
39A THR* 1.3 64.0 + - - +
40A MET* 3.4 32.9 - - - +
46A ARG* 5.2 4.2 - - - +
48A VAL* 3.8 24.7 - - + +
50A ASP 3.2 10.1 - - - +
51A ASP* 3.6 25.0 + - - +
53A ARG* 6.2 1.6 - - - +
148A VAL 3.8 0.7 - - - +
149A PHE* 3.4 2.9 - - - -
150A VAL* 2.8 57.8 + - + +
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Residues in contact with THR 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 PHE* 3.3 11.8 - - - -
38A ARG* 1.3 73.3 - - - +
40A MET* 1.3 59.8 + - - +
48A VAL* 3.5 4.3 - - - +
49A ILE* 2.7 42.0 + - + -
50A ASP 2.8 13.1 + - - -
97A TYR* 2.9 40.0 + - + -
147A LEU* 4.4 7.6 - - + -
148A VAL 3.6 4.3 - - - +
149A PHE* 3.0 36.4 - - + -
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Residues in contact with MET 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 ARG* 3.4 34.8 - - + +
39A THR* 1.3 79.6 - - - +
41A LYS* 1.3 66.8 + - - +
46A ARG* 3.3 44.9 - - + +
47A THR 3.2 7.0 - - - +
48A VAL* 3.7 15.5 - - + -
49A ILE* 4.5 1.1 - - - +
147A LEU* 3.4 10.1 - - - +
148A VAL* 2.7 63.9 + - + +
150A VAL* 3.8 28.9 - - + -
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Residues in contact with LYS 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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40A MET* 1.3 84.8 - - - +
42A CYS* 1.3 59.0 + - - +
43A ASP* 3.3 35.4 + - - +
46A ARG* 3.9 11.3 - - - +
47A THR* 2.9 29.4 + - - +
49A ILE* 3.5 27.6 - - + +
136A ASP* 6.5 0.9 - - - -
139A GLU* 6.4 0.2 - - - +
140A LEU* 4.7 5.2 - - + +
145A GLN* 3.5 31.6 - - - +
146A PRO 4.6 0.7 - - - -
147A LEU* 4.3 8.5 - - + -
148A VAL* 4.2 3.5 - - - +
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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