Contacts of the strand formed by residues 75 - 91 (chain A) in PDB entry 3BUK
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 TRP 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ASN* 5.7 1.6 - - - +
70A ILE* 4.1 10.5 - - + +
71A ASP* 3.0 19.2 + - + +
72A ASP* 3.5 23.1 + - - +
73A LYS 3.7 0.8 - - - -
74A HIS* 1.3 85.3 - - + +
76A ASN* 1.3 68.5 - - - +
77A SER* 4.0 1.4 + - - -
112A LEU* 4.1 21.8 - - + -
113A SER 3.6 20.6 - - - -
114A ARG* 3.9 23.1 - - + -
115A LYS* 3.8 8.1 - - - -
11B TYR* 4.2 21.8 - + - -
68B ARG* 5.4 0.9 - - + -
69B GLY* 3.6 33.4 - - - -
135C PRO* 4.0 16.2 - - + -
136C CYS 4.0 17.0 - - - -
137C LEU* 4.4 11.2 - - + -
138C PRO* 3.8 32.3 - - + +
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Residues in contact with ASN 76 (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 ASN* 5.3 3.8 - - - +
75A TRP* 1.3 79.5 - - - +
77A SER* 1.3 64.1 + - - +
112A LEU* 3.4 4.0 - - - -
113A SER* 2.8 51.6 + - - +
114A ARG 4.5 7.5 + - - -
115A LYS* 3.7 23.7 - - - +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASN* 3.5 9.9 + - - +
66A GLY* 3.3 18.1 + - - -
67A CYS* 2.9 33.1 + - - -
70A ILE* 3.9 23.6 - - - +
72A ASP* 6.0 1.0 - - - +
75A TRP 4.8 1.2 + - - -
76A ASN* 1.3 79.7 - - - +
78A GLN* 1.3 69.9 + - - +
110A CYS* 4.0 1.8 - - - -
111A ALA 3.3 9.4 - - - -
112A LEU* 4.0 3.6 - - - -
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Residues in contact with GLN 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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60A ALA* 3.7 26.6 - - + +
61A ARG* 6.4 0.2 - - + -
66A GLY* 5.9 0.2 - - - -
67A CYS* 3.5 7.5 - - - +
77A SER* 1.3 80.3 - - - +
79A CYS* 1.3 64.8 + - - +
80A LYS* 3.5 36.5 + - + +
109A VAL 3.5 0.2 - - - +
110A CYS* 3.3 2.9 - - - -
111A ALA* 2.8 35.2 + - + +
10B GLU* 5.1 1.4 + - - -
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Residues in contact with CYS 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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14A CYS* 2.0 46.9 - - - -
15A ASP 4.8 0.2 - - - -
57A CYS* 3.6 6.0 - - - +
59A GLU 3.5 17.5 - - - +
60A ALA* 2.9 25.2 + - - +
62A PRO* 3.5 29.6 - - - -
67A CYS* 3.9 6.3 - - - -
78A GLN* 1.3 73.1 - - - +
80A LYS* 1.3 61.2 + - - +
108A CYS* 3.6 12.1 - - - -
109A VAL 3.4 4.7 - - - -
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Residues in contact with LYS 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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57A CYS* 3.3 4.9 - - - -
78A GLN* 3.5 35.7 + - + +
79A CYS* 1.3 75.5 - - - +
81A THR* 1.3 67.2 + - - +
82A SER* 3.5 1.3 + - - -
109A VAL* 2.8 42.7 + - + +
111A ALA* 4.4 11.0 - - + -
10B GLU* 3.4 32.5 + - - +
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Residues in contact with THR 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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56A ARG* 3.5 11.2 - - + +
57A CYS* 3.0 30.3 + - - +
79A CYS 4.3 0.2 + - - -
80A LYS* 1.3 76.2 - - - +
82A SER* 1.3 63.5 + - - +
83A GLN* 4.3 2.4 + - + +
105A ASP* 3.6 41.3 - - + +
107A SER 3.4 11.0 - - - +
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Residues in contact with SER 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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80A LYS* 3.5 1.6 + - - -
81A THR* 1.3 76.0 - - - +
83A GLN* 1.3 67.9 + - - +
105A ASP* 3.7 1.4 - - - -
106A THR* 2.9 25.2 + - - +
107A SER* 2.5 38.9 + - - +
109A VAL* 4.0 18.7 - - - +
5B LYS* 6.1 5.2 - - - -
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Residues in contact with GLN 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 THR* 5.3 1.8 - - + +
82A SER* 1.3 81.8 - - - +
84A THR* 1.3 63.1 + - - +
103A ARG* 3.5 50.1 + - + +
104A ILE* 3.0 27.9 - - - +
105A ASP* 3.1 26.1 + - - +
106A THR* 4.2 2.2 - - - +
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Residues in contact with THR 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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83A GLN* 1.3 75.2 + - - +
85A TYR* 1.3 74.4 + - - +
86A VAL* 4.0 9.1 + - + -
102A ILE 3.4 0.2 - - - +
103A ARG* 3.4 7.1 - - - +
104A ILE* 2.8 33.0 + - + +
106A THR* 3.8 29.1 - - - +
53B TYR* 3.2 31.0 - - + +
55B THR* 3.5 14.7 - - - +
106B THR* 3.8 9.9 - - - +
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Residues in contact with TYR 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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29A ASP 5.0 0.5 + - - -
30A ILE* 3.6 53.4 + - + +
84A THR* 1.3 83.3 + - - +
86A VAL* 1.3 66.7 + - - +
101A TRP* 3.6 21.1 - - + -
102A ILE 3.1 23.6 - - - +
103A ARG* 3.5 52.4 + - + -
20B TRP* 4.8 0.4 - - + -
53B TYR* 3.6 51.9 + + + +
68C SER 5.4 0.2 - - - -
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Residues in contact with VAL 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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52A PHE* 3.7 26.7 - - + -
84A THR* 4.8 6.7 - - + -
85A TYR* 1.3 78.9 - - - +
87A ARG* 1.3 77.2 + - - +
101A TRP* 3.3 9.0 - - - -
102A ILE* 2.8 33.7 + - + +
104A ILE* 3.7 26.7 - - + -
86B VAL* 4.2 33.7 - - + -
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Residues in contact with ARG 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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50A GLN* 4.4 1.7 + - - -
52A PHE* 4.1 3.6 - - - -
86A VAL* 1.3 87.1 - - - +
88A ALA* 1.3 59.8 + - - +
99A TRP* 3.6 58.1 + - + +
100A ARG* 3.4 9.3 - - - +
101A TRP* 3.2 57.6 - - + +
41B ILE* 6.0 1.2 - - - +
48B VAL* 4.1 6.4 - - - +
49B LYS 3.2 25.9 + - - -
51B TYR* 3.4 17.2 + - - +
86B VAL* 5.9 1.6 - - - +
41C ASP* 3.3 27.3 + - - -
72C VAL* 4.6 7.3 - - - +
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Residues in contact with ALA 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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37A VAL* 4.7 1.6 - - + -
50A GLN* 3.4 13.9 - - - +
52A PHE* 3.9 6.7 - - + -
87A ARG* 1.3 77.7 - - - +
89A LEU* 1.3 63.7 + - - +
90A THR* 3.4 17.2 - - + +
99A TRP* 3.3 9.4 - - - -
100A ARG 2.9 30.3 + - - +
102A ILE* 3.4 32.1 - - + -
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Residues in contact with LEU 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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37A VAL* 4.0 0.2 - - - -
38A LEU* 3.1 32.9 + - + +
40A GLU 3.6 22.2 - - - +
41A ILE* 3.9 23.6 - - + -
42A LYS* 4.7 3.4 - - + +
50A GLN* 2.9 34.4 - - - +
88A ALA* 1.3 70.0 - - - +
90A THR* 1.3 62.7 + - - +
97A VAL* 4.9 5.2 - - + -
98A GLY* 3.5 31.2 - - - +
99A TRP* 3.9 26.3 - - + +
43B THR* 5.8 1.8 - - - +
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Residues in contact with THR 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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35A VAL* 3.7 21.1 - - + -
36A THR 3.1 16.2 - - - +
37A VAL* 4.3 5.2 - - + -
38A LEU* 3.6 6.7 - - - -
88A ALA* 3.4 24.0 - - + +
89A LEU* 1.3 81.8 - - - +
91A SER* 1.3 61.7 + - - +
97A VAL* 3.1 5.0 - - - +
98A GLY 2.8 36.3 + - - -
100A ARG* 2.8 37.4 + - + +
102A ILE* 4.5 5.8 - - + -
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Residues in contact with SER 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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35A VAL* 3.6 4.2 - - - +
36A THR* 2.9 46.1 + - - +
38A LEU* 3.9 8.2 - - - +
90A THR* 1.3 76.0 - - - +
92A GLU* 1.3 61.3 + - - +
93A ASN 4.1 0.2 - - - -
94A ASN* 3.7 25.7 + - - -
95A LYS 4.4 0.4 - - - -
96A LEU 4.2 3.8 - - - -
97A VAL* 3.9 22.0 - - - -
100A ARG* 3.7 7.9 - - - +
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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