Contacts of the strand formed by residues 77 - 92 (chain A) in PDB entry 1B8M
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 ASN 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ILE* 5.0 0.9 - - - -
76A TRP* 1.3 83.1 - - - +
78A SER* 1.3 63.7 + - - +
113A LEU* 3.4 5.2 - - - +
114A THR* 2.8 47.2 + - + +
115A ILE 3.4 17.4 + - - -
116A LYS* 3.4 24.8 - - - +
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Residues in contact with SER 78 (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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66A GLU 4.1 5.0 - - - +
67A GLY* 3.3 15.2 - - - -
68A CYS* 2.7 44.8 + - - -
71A ILE* 3.8 21.0 - - - +
77A ASN* 1.3 78.8 - - - +
79A GLN* 1.3 67.8 + - - +
111A CYS* 3.8 1.6 - - - -
112A THR 3.2 9.9 - - - -
113A LEU* 4.2 2.0 - - - -
114A THR* 5.1 2.5 - - - +
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Residues in contact with GLN 79 (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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65A LYS 5.7 4.9 - - - +
66A GLU 5.9 0.9 - - - +
67A GLY* 4.8 3.8 - - - -
68A CYS* 3.6 4.5 - - - -
78A SER* 1.3 79.2 - - - +
80A CYS* 1.3 67.7 + - - +
81A ARG* 3.1 44.4 + - - +
110A VAL 3.7 0.7 - - - +
111A CYS* 3.5 1.4 - - - -
112A THR* 3.0 34.5 + - + +
114A THR* 6.0 5.5 - - + +
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Residues in contact with CYS 80 (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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13A CYS* 2.0 59.2 - - + -
58A CYS* 3.6 9.4 - - + +
64A THR* 3.5 32.9 + - - +
65A LYS 5.8 1.0 + - - -
67A GLY 5.2 0.2 - - - -
68A CYS* 3.7 13.4 - - - +
79A GLN* 1.3 76.1 - - - +
81A ARG* 1.3 62.6 + - - +
109A CYS* 4.0 8.5 - - - -
110A VAL 3.6 0.4 - - - -
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Residues in contact with ARG 81 (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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58A CYS* 3.3 6.9 - - - -
79A GLN* 3.1 39.9 - - + +
80A CYS* 1.3 77.8 - - - +
82A THR* 1.3 68.3 + - - +
83A THR* 3.5 7.2 + - + +
110A VAL* 2.9 33.1 + - + +
112A THR* 3.6 32.9 + - - +
114A THR* 6.0 2.6 - - - -
13B GLU* 3.2 34.2 + - - +
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Residues in contact with THR 82 (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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57A LYS* 3.7 18.2 - - + +
58A CYS* 3.3 23.6 + - - +
81A ARG* 1.3 77.1 - - - +
83A THR* 1.3 64.6 + - - +
84A GLN* 5.4 2.1 - - - +
106A ASP* 3.6 36.3 - - + +
108A SER 3.3 13.7 - - - +
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Residues in contact with THR 83 (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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81A ARG* 3.9 4.7 - - + +
82A THR* 1.3 79.3 - - - +
84A GLN* 1.3 68.9 + - - +
106A ASP* 3.9 3.3 - - - -
107A THR* 3.1 22.7 + - - -
108A SER* 2.5 39.1 + - - +
110A VAL* 3.3 32.2 - - + +
117B THR 5.2 0.5 + - - -
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Residues in contact with GLN 84 (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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82A THR 5.4 1.6 - - - +
83A THR* 1.3 83.8 + - - +
85A SER* 1.3 63.2 - - - +
104A ARG* 3.0 56.2 - - + +
105A ILE* 3.4 12.7 - - - +
106A ASP* 3.9 19.1 - - - +
107A THR* 3.9 1.3 + - - -
59B THR* 5.8 0.2 + - - -
117B THR 5.6 0.2 - - - +
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Residues in contact with SER 85 (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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84A GLN* 1.3 74.3 - - - +
86A TYR* 1.3 72.2 + - - +
87A VAL 3.8 0.5 + - - -
104A ARG* 3.4 3.8 - - - +
105A ILE* 3.1 29.9 + - - +
107A THR* 3.1 32.3 - - - -
57B PHE* 4.0 21.2 + - - -
58B GLU* 5.3 0.2 - - - -
59B THR* 4.5 5.9 + - - -
117B THR* 4.0 20.2 - - - +
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Residues in contact with TYR 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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30A ASP 4.2 0.7 - - - -
31A MET* 3.5 53.7 + - + -
85A SER* 1.3 78.7 + - - +
87A VAL* 1.3 59.6 + - - +
102A PHE* 3.8 26.8 - - + -
103A ILE 3.4 17.0 - - - -
104A ARG* 3.4 46.0 + - + -
57B PHE* 3.8 49.8 + + + +
115B ILE* 5.6 2.8 - - - +
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Residues in contact with VAL 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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53A PHE* 4.1 17.0 - - + -
86A TYR* 1.3 74.9 - - - +
88A ARG* 1.3 68.2 + - - +
102A PHE* 3.8 4.3 - - - -
103A ILE* 2.9 36.1 + - + +
105A ILE* 3.4 48.2 - - + -
107A THR* 6.1 0.9 - - + -
96B TYR 5.5 0.9 - - - +
97B VAL* 3.9 31.0 - - + -
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Residues in contact with ARG 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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53A PHE* 4.5 3.1 - - - -
87A VAL* 1.3 84.8 - - - +
89A ALA* 1.3 63.5 + - - +
100A TRP* 3.3 53.0 + - + +
101A ARG 3.2 9.4 - - - +
102A PHE* 3.5 48.4 - - + -
52B LEU* 4.2 16.0 - - - +
53B ARG 3.1 26.7 + - - -
54B GLN* 5.1 0.4 - - - +
55B TYR* 3.6 25.2 + - - +
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Residues in contact with ALA 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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38A VAL* 5.0 1.3 - - + -
51A GLN* 3.3 15.0 - - - +
53A PHE* 3.6 23.3 - - + -
88A ARG* 1.3 76.2 - - - +
90A LEU* 1.3 60.8 + - - +
91A THR* 3.2 12.3 + - + +
100A TRP* 3.4 10.6 - - - -
101A ARG 2.9 29.8 + - - +
103A ILE* 3.6 19.5 - - + -
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Residues in contact with LEU 90 (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 VAL* 4.0 0.3 - - - +
39A LEU* 3.2 35.3 + - + +
41A LYS 4.0 2.0 - - - +
42A VAL* 3.6 25.1 - - + -
43A PRO* 3.5 32.3 - - + -
51A GLN* 2.9 26.7 + - - +
89A ALA* 1.3 66.9 - - - +
91A THR* 1.3 60.4 + - - +
98A ILE* 4.0 15.7 - - + -
99A GLY* 3.7 21.3 - - - +
100A TRP* 3.6 32.5 - - + +
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Residues in contact with THR 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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36A VAL* 3.7 28.5 - - + -
37A THR 3.2 10.5 - - - +
38A VAL* 4.1 11.2 - - + -
39A LEU* 4.4 2.9 - - - -
89A ALA* 3.7 10.5 - - + +
90A LEU* 1.3 79.3 - - - +
92A MET* 1.3 63.3 + - - +
98A ILE* 3.4 7.6 - - - +
99A GLY 2.8 39.1 + - - -
101A ARG* 2.9 26.7 + - + +
103A ILE* 3.7 17.5 - - + -
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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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36A VAL* 4.5 1.3 - - - -
37A THR* 2.8 51.7 + - + +
39A LEU* 3.8 22.0 - - + -
91A THR* 1.3 74.8 - - - +
93A ASP* 1.3 66.6 + - - +
96A LYS* 3.6 45.8 - - - +
97A ARG 3.4 4.9 - - - -
98A ILE* 3.4 27.6 - - + -
101A ARG* 4.2 0.4 - - - -
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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