Contacts of the strand formed by residues 3 - 12 (chain A) in PDB entry 5U2V
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 HIS 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A MET* 3.9 15.3 - - + +
1A ARG* 3.3 47.4 + - + +
2A THR* 1.3 76.2 + - - +
4A SER* 1.3 62.9 + - - +
29A ASP* 2.5 35.3 + - - +
99A GLU* 3.3 5.2 - - - +
100A LEU* 2.8 36.3 + - + +
165A LEU* 3.7 9.4 - - + +
169A LEU* 3.5 46.1 - - + +
176A LEU 3.5 23.9 + - - -
177A GLN* 4.5 4.0 - - - +
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Residues in contact with SER 4 (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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2A THR* 5.8 0.2 - - - -
3A HIS* 1.3 77.1 - - - +
5A LEU* 1.3 61.6 + - - +
6A ARG* 4.2 19.1 + - - -
28A VAL* 3.3 10.0 - - - +
29A ASP* 2.9 44.8 + - - -
98A CYS 3.2 12.1 - - - -
99A GLU* 3.7 20.0 - - - -
109A PHE* 5.6 0.9 - - - -
165A LEU* 3.9 5.2 - - - -
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Residues in contact with LEU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 1.3 72.8 - - - +
6A ARG* 1.3 64.0 + - - +
7A TYR* 3.7 37.0 - - + +
27A TYR 3.3 17.5 - - - +
28A VAL* 4.1 7.9 - - + -
33A ILE* 4.0 12.3 - - + -
97A GLY* 2.9 5.9 - - - -
98A CYS* 2.8 37.4 + - - +
156A TRP* 5.3 0.2 - - + -
161A CYS* 3.5 32.5 - - - +
164A TRP* 3.7 21.1 - - + -
165A LEU* 3.8 20.3 - - + +
168A PHE* 4.2 2.9 - - + -
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Residues in contact with ARG 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 4.2 14.6 + - - +
5A LEU* 1.3 78.1 - - - +
7A TYR* 1.3 63.7 + - - +
8A PHE* 3.6 42.9 - - + -
25A VAL 4.0 0.7 - - - +
26A GLY* 3.3 2.4 - - - -
27A TYR* 2.8 57.1 + - + +
29A ASP 2.8 30.1 + - - -
30A SER* 4.3 4.8 - - - +
95A MET* 4.7 7.0 - - + -
96A ILE 3.3 6.7 - - - +
109A PHE* 3.9 23.6 - - + -
56B PHE 3.7 11.7 + - - -
57B SER* 5.0 0.4 - - - +
58B LYS* 4.6 10.2 - - - +
63B TYR* 5.3 4.6 + - - -
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Residues in contact with TYR 7 (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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5A LEU* 3.7 29.2 - - + +
6A ARG* 1.3 74.6 - - - +
8A PHE* 1.3 64.4 + - - +
9A ARG* 5.6 2.4 - - + +
24A SER* 5.3 6.1 - - - +
25A VAL 3.6 2.0 - - - -
26A GLY* 3.5 19.5 - - - -
33A ILE* 4.1 2.6 - - + +
34A THR* 3.8 21.6 - - + +
43A LYS* 5.1 7.9 - - - -
94A ARG* 3.7 1.8 + - - +
95A MET* 3.3 3.6 - - - +
96A ILE* 2.7 60.0 + - + +
97A GLY* 5.9 0.7 - - - -
156A TRP* 4.5 16.8 - + - -
164A TRP* 5.2 5.3 - + + +
168A PHE* 3.5 29.1 - - - -
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Residues in contact with PHE 8 (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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6A ARG* 3.6 41.7 - - + -
7A TYR* 1.3 77.1 - - - +
9A ARG* 1.3 63.9 + - - +
24A SER* 3.0 22.5 + - - -
25A VAL 3.0 19.3 + - - +
27A TYR* 3.7 25.1 - + - -
93A GLN* 5.9 2.0 - - + -
94A ARG 3.1 6.7 - - - -
95A MET* 3.5 43.3 - - + -
56B PHE* 3.5 43.3 - + + -
57B SER 3.7 22.2 - - - -
58B LYS* 4.4 0.2 - - - -
60B TRP* 4.7 8.5 - + - -
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Residues in contact with ARG 9 (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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7A TYR* 5.6 2.7 - - + +
8A PHE* 1.3 82.7 - - - +
10A LEU* 1.3 60.9 + - - +
22A PHE* 4.0 20.4 - - + -
23A ILE 3.4 4.5 - - - -
24A SER* 3.8 12.2 + - - +
69A TRP* 3.5 54.5 + - - +
72A MET* 4.6 14.8 - - - -
73A PHE* 3.6 33.6 - - + -
93A GLN* 3.2 9.9 - - - +
94A ARG* 2.8 78.4 + - + +
112A TYR* 5.1 1.4 + - - -
56B PHE* 5.2 1.0 - - - -
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Residues in contact with LEU 10 (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 ARG* 1.3 74.4 - - - +
11A GLY* 1.3 70.7 + - - +
12A VAL* 4.1 15.7 - - + +
19A VAL* 5.7 0.4 - - + -
20A PRO 6.0 0.7 - - - +
21A GLU 3.8 0.5 - - - +
22A PHE* 3.2 6.5 - - - -
23A ILE* 2.8 51.0 + - + +
73A PHE* 3.9 3.1 - - - -
91A THR* 4.2 9.2 - - + -
92A TYR 3.6 0.7 - - - -
93A GLN* 3.5 27.6 - - + -
33B SER* 4.0 23.1 - - - +
54B LEU* 4.5 6.3 - - + -
56B PHE* 3.6 30.3 - - + -
62B PHE* 4.1 13.0 - - + -
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Residues in contact with GLY 11 (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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10A LEU* 1.3 74.5 - - - +
12A VAL* 1.3 61.4 + - - +
21A GLU 3.3 7.0 - - - -
22A PHE* 4.6 2.0 - - - -
73A PHE* 3.3 18.8 - - - -
77A LEU* 3.8 9.7 - - - +
91A THR* 3.3 7.3 - - - -
92A TYR 2.7 39.2 + - - -
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Residues in contact with VAL 12 (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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10A LEU* 4.1 24.7 - - + -
11A GLY* 1.3 77.1 - - - +
13A SER* 1.3 73.7 + - - +
15A PRO* 3.6 28.0 - - + +
19A VAL* 4.1 21.3 - - + -
20A PRO 3.9 13.5 - - - +
21A GLU* 2.8 27.0 + - - +
77A LEU* 4.1 2.7 - - - -
89A SER* 3.7 10.1 - - - +
90A HIS 3.6 4.7 - - - +
91A THR* 4.4 10.5 - - + -
33B SER* 4.5 4.3 - - - +
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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