Contacts of the strand formed by residues 92 - 102 (chain A) in PDB entry 4ZFO
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 ALA 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 4.1 13.7 - - - -
39A ARG 3.5 17.3 - - - +
40A ALA* 3.7 12.8 - - + +
41A PRO* 4.4 3.4 - - - -
90A ASP 3.3 4.9 + - - +
91A THR* 1.3 77.4 - - - +
93A LEU* 1.3 63.5 + - - +
94A TYR* 3.4 20.6 - - + -
115A SER* 3.7 1.6 - - - -
116A VAL 2.9 32.5 + - - +
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Residues in contact with LEU 93 (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* 3.1 4.3 - - - +
39A ARG* 2.8 43.6 + - + +
92A ALA* 1.3 72.1 - - - +
94A TYR* 1.3 60.4 + - - +
95A TYR* 3.3 36.7 - - + +
113A GLY* 5.0 3.1 - - - -
114A THR 3.5 6.3 - - - +
115A SER* 3.6 35.0 - - - +
41B ARG* 5.5 10.5 - - - +
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Residues in contact with TYR 94 (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 GLN* 2.9 9.0 + - - -
20A LEU* 3.5 20.9 - - + -
36A TRP* 4.5 5.2 - + + -
37A VAL 3.6 2.2 - - - +
38A ARG* 3.0 36.2 + - + -
48A ILE* 3.6 24.0 - - + -
68A PHE* 4.0 12.5 - + - -
81A LEU* 3.7 15.7 - - + -
83A MET* 3.3 16.2 - - + +
90A ASP* 2.5 29.9 + - - -
92A ALA* 3.4 22.9 - - + -
93A LEU* 1.3 73.5 - - - +
95A TYR* 1.3 61.3 + - - +
113A GLY* 3.3 1.7 - - - -
114A THR* 2.8 41.1 + - - +
116A VAL* 3.8 18.6 - - + -
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Residues in contact with TYR 95 (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 GLN* 3.6 2.5 - - - +
36A TRP* 3.4 8.4 - - - -
37A VAL* 2.8 55.1 + - + +
38A ARG* 4.7 2.2 - - - -
39A ARG* 4.4 8.5 - - + +
45A LEU* 5.1 0.4 - - + -
93A LEU* 3.3 48.9 - - + +
94A TYR* 1.3 73.1 - - - +
96A CYS* 1.3 61.0 + - - +
110A TRP* 4.3 12.8 - - + -
111A GLY 3.9 3.8 - - - +
112A GLN 3.9 3.8 - - - -
113A GLY* 3.6 23.1 - - - -
38B GLN* 3.5 27.5 + - - -
41B ARG 5.2 0.9 + - - -
42B GLN 3.5 9.4 + - - -
43B SER* 3.5 34.8 - - - -
44B PRO* 3.8 8.5 - - + -
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Residues in contact with CYS 96 (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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4A LEU* 4.0 2.5 - - - -
6A GLN* 3.4 22.7 + - - -
22A CYS* 2.1 54.5 - - + -
34A MET* 5.0 0.2 - - + -
35A SER 3.2 5.2 - - - -
36A TRP* 3.8 8.4 - - + -
79A LEU* 3.7 14.8 - - + -
95A TYR* 1.3 75.2 - - - +
97A ALA* 1.3 64.9 + - - +
110A TRP* 3.5 6.1 - - - -
111A GLY* 3.0 30.8 + - - -
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Residues in contact with ALA 97 (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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4A LEU* 4.0 1.6 - - - -
34A MET* 3.6 11.5 - - - +
35A SER* 2.8 44.5 + - - +
37A VAL* 6.0 1.6 - - + -
96A CYS* 1.3 77.9 - - - +
98A SER* 1.3 61.7 + - - +
99A LEU* 4.1 8.1 - - + -
109A TYR 3.2 12.8 - - - +
110A TRP* 3.5 33.2 - - + -
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Residues in contact with SER 98 (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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4A LEU* 4.0 4.4 - - - +
27A ILE* 4.4 14.1 - - - -
32A TYR* 3.5 20.6 - - - +
33A TRP 3.4 16.2 + - - -
34A MET* 3.6 17.3 - - - -
97A ALA* 1.3 74.1 - - - +
99A LEU* 1.3 61.6 + - - +
100A TYR* 3.5 15.5 + - - -
107A MET 3.8 1.0 - - - +
108A ASP* 3.4 4.3 - - - -
109A TYR* 2.9 32.8 + - - -
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Residues in contact with LEU 99 (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 TRP* 4.3 12.1 + - - +
35A SER* 4.7 16.4 + - - +
97A ALA* 4.1 8.9 + - + -
98A SER* 1.3 76.1 + - - +
100A TYR* 1.3 64.2 + - - +
107A MET 3.4 3.4 - - - +
108A ASP* 3.5 28.5 - - + -
110A TRP* 4.2 19.1 - - + -
36B TYR* 3.7 24.7 - - + +
46B ALA* 4.5 6.1 - - + -
55B PHE* 4.5 2.2 - - + -
89B GLN* 6.2 0.2 - - - +
17F LEU* 3.9 29.1 - - + +
18F LEU* 3.8 27.8 - - + +
19F HIS* 5.1 3.1 - - - -
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Residues in contact with TYR 100 (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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27A ILE* 3.4 16.9 - - + +
32A TYR* 3.4 61.8 + + + -
33A TRP 5.8 0.4 - - - +
98A SER* 3.5 23.1 - - - -
99A LEU* 1.3 74.6 - - - +
101A TYR* 1.3 61.2 + - - +
102A ASP* 3.7 13.9 - - + -
103A TYR* 5.8 1.8 - + - -
106A ALA* 3.4 3.1 - - - -
107A MET* 2.7 69.4 + - + +
109A TYR* 3.3 32.7 + + - -
18F LEU* 3.7 18.6 - - - +
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Residues in contact with TYR 101 (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 TYR* 5.1 1.7 - - - -
100A TYR* 1.3 76.8 - - - +
102A ASP* 1.3 67.2 + - - +
104A GLY* 3.6 31.2 + - - -
105A ASP* 3.4 26.5 - - - -
106A ALA* 3.6 11.9 - - + -
49B PHE* 4.9 2.0 - + - -
18F LEU* 3.9 14.3 + - + +
20F ALA* 3.7 25.0 - - + +
21F CYS 4.0 22.4 - - - -
22F ILE* 3.7 14.8 - - + -
23F PRO* 3.3 28.9 - - + +
26F LEU* 4.3 16.0 - - + +
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Residues in contact with ASP 102 (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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31A ARG* 2.8 29.7 + - - -
32A TYR* 2.5 36.6 + - + +
100A TYR* 3.7 13.4 - - + -
101A TYR* 1.3 79.1 - - - +
103A TYR* 1.3 93.8 + - + +
104A GLY 3.1 2.2 - - - -
105A ASP* 3.1 21.4 + - - +
107A MET* 4.8 4.0 - - - +
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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