Contacts of the strand formed by residues 84 - 95 (chain A) in PDB entry 4MOB
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 SER 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A PHE* 2.8 41.1 + - - +
83A THR* 1.3 81.8 - - - +
85A MET* 1.3 64.0 + - - +
110A THR* 4.1 13.1 - - - +
111A PHE 3.2 10.3 - - - -
112A VAL* 4.0 12.8 - - - +
123A LEU* 3.5 4.8 - - - +
144A ARG* 3.8 4.0 + - - -
401A COA 2.8 34.3 + - - -
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ALA* 3.6 21.3 - - + +
46A HIS* 3.8 25.6 - - - -
47A ALA* 3.6 13.9 - - + -
51A CYS* 3.6 32.3 - - + -
77A VAL* 3.9 8.7 - - + -
79A ARG 3.3 14.1 - - - +
80A ALA* 3.8 6.5 - - - -
81A PHE* 4.3 2.5 - - - -
84A SER* 1.3 75.3 - - - +
86A GLU* 1.3 59.7 + - - +
87A ILE* 3.4 19.8 - - + +
110A THR* 3.4 8.1 - - - +
111A PHE 2.8 42.5 + - - +
113A ALA* 4.5 6.5 - - + +
123A LEU* 4.3 15.9 - - + -
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Residues in contact with GLU 86 (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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77A VAL* 3.6 5.2 - - - +
78A THR* 2.7 46.8 + - - +
79A ARG 3.0 11.2 + - - +
81A PHE* 4.1 13.3 - - + -
85A MET* 1.3 71.4 - - - +
87A ILE* 1.3 65.0 + - - +
108A PHE* 3.6 13.9 - - + -
109A SER 3.7 4.5 - - - +
110A THR* 4.6 3.1 - - - +
140A ALA* 3.3 12.1 - - + +
143A ARG* 2.7 40.4 + - - +
147A ARG* 2.5 47.9 + - - +
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Residues in contact with ILE 87 (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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39A ALA* 3.6 44.9 - - + +
42A ALA* 4.4 2.7 - - + -
43A ALA* 3.8 20.4 - - + +
75A ALA* 3.9 5.4 - - + -
76A LYS 3.3 10.8 - - - +
77A VAL* 4.5 4.0 - - + -
85A MET* 3.4 35.2 - - + +
86A GLU* 1.3 80.1 - - - +
88A SER* 1.3 72.3 + - - +
89A ILE* 3.7 6.4 - - + +
108A PHE* 3.2 6.4 - - - -
109A SER 2.7 40.3 + - - +
111A PHE* 3.9 10.5 - - + -
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Residues in contact with SER 88 (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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74A LYS 3.8 0.7 - - - +
75A ALA* 3.2 4.5 - - - -
76A LYS* 2.9 36.7 + - - +
78A THR* 3.6 18.2 - - - +
87A ILE* 1.3 75.1 - - - +
89A ILE* 1.3 61.5 + - - +
106A VAL* 6.5 0.9 - - - -
107A ALA 3.4 4.7 - - - -
108A PHE* 3.4 28.3 - - - -
136A GLU* 5.9 0.4 - - - -
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Residues in contact with ILE 89 (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* 3.9 26.9 - - + +
39A ALA* 4.1 9.9 - - + -
73A ILE* 3.6 28.3 - - + -
74A LYS 3.3 5.6 - - - +
75A ALA* 4.0 7.2 - - + -
87A ILE* 3.7 29.4 - - + +
88A SER* 1.3 79.5 - - - +
90A LYS* 1.3 66.9 + - - +
91A VAL* 4.3 5.8 - - + -
105A SER 4.1 0.4 - - - +
106A VAL* 3.4 6.6 - - - +
107A ALA* 2.8 48.8 + - + +
108A PHE 4.1 2.0 - - - +
109A SER* 3.9 24.2 - - - +
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A THR 3.7 1.2 - - - +
73A ILE* 3.5 4.7 - - - +
74A LYS* 2.9 54.7 + - + +
89A ILE* 1.3 75.4 - - - +
91A VAL* 1.3 64.3 + - - +
92A MET* 3.6 34.6 - - + +
103A LEU* 4.0 20.9 - - + -
105A SER 3.6 3.6 - - - +
106A VAL* 4.4 12.6 - - + -
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Residues in contact with VAL 91 (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 LEU* 4.3 7.2 - - + -
35A ILE* 3.8 33.4 - - + -
71A ILE* 4.1 22.9 - - + -
72A THR 3.5 2.9 - - - +
73A ILE* 3.9 9.2 - - + -
89A ILE* 4.3 6.7 - - + -
90A LYS* 1.3 77.4 - - - +
92A MET* 1.3 66.4 + - - +
103A LEU* 3.7 4.3 - - - +
104A VAL* 2.7 53.8 + - + -
105A SER* 2.8 25.7 + - - +
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Residues in contact with MET 92 (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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71A ILE* 3.6 4.0 - - - -
72A THR* 3.0 41.7 + - + +
74A LYS* 6.1 3.1 - - + -
90A LYS* 3.6 38.6 - - + +
91A VAL* 1.3 78.6 - - - +
93A VAL* 1.3 60.6 + - - +
101A GLU* 3.6 31.9 - - + +
102A LYS* 3.3 34.3 - - - +
103A LEU* 3.5 18.8 - - + +
104A VAL* 3.9 2.5 - - - -
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Residues in contact with VAL 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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63A GLU* 4.6 10.5 - - + -
65A ALA* 3.7 16.8 - - + -
69A GLN* 3.6 37.9 - - + +
70A VAL 3.5 7.0 - - - +
71A ILE* 4.1 5.6 - - + -
92A MET* 1.3 75.3 - - - +
94A GLN* 1.3 63.6 + - - +
100A ILE 3.8 1.0 - - - +
101A GLU* 3.1 6.1 - - - +
102A LYS* 2.9 56.4 + - + +
104A VAL* 3.6 19.1 - - + -
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Residues in contact with GLN 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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69A GLN* 3.2 7.4 - - - +
70A VAL* 2.9 39.2 + - + +
72A THR* 6.1 0.7 - - - +
93A VAL* 1.3 77.8 - - - +
95A ASP* 1.3 72.3 + - - +
96A MET* 3.6 25.5 + - - +
99A GLY* 3.2 28.2 + - - +
100A ILE 3.4 2.5 - - - -
101A GLU* 3.8 26.6 + - + +
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Residues in contact with ASP 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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69A GLN* 3.2 34.5 + - - +
94A GLN* 1.3 73.5 - - - +
96A MET* 1.3 59.7 + - - +
97A LEU* 3.0 16.1 + - - +
98A THR* 2.9 47.9 + - - +
99A GLY* 2.8 30.3 + - - -
100A ILE* 2.9 13.4 + - + +
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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