Contacts of the strand formed by residues 98 - 114 (chain B) 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 GLY 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU* 3.9 13.5 - - - +
90B THR* 2.8 36.2 + - - -
96B LEU 3.3 3.0 + - - -
97B VAL* 1.3 74.3 - - - +
99B TRP* 1.3 65.9 + - - -
100B ARG* 4.3 3.1 - - - -
73D GLU* 5.0 10.1 - - - -
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Residues in contact with TRP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.6 17.4 - - + +
43A THR* 4.3 8.9 + - - -
48A VAL* 3.8 36.0 - - + +
99A TRP* 3.5 39.5 - + - -
41B ILE* 4.1 29.6 - - + -
50B GLN* 4.3 3.1 - - - -
87B ARG* 3.4 51.0 + - + +
88B ALA* 3.2 24.9 - - - -
89B LEU* 3.9 27.7 - - + +
98B GLY* 1.3 77.5 - - - -
100B ARG* 1.3 65.1 - - - +
72D VAL* 4.4 12.5 - - - +
73D GLU* 5.6 1.0 + - - -
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 3.7 28.9 + - + +
35B VAL* 4.1 12.4 - - - +
87B ARG* 3.4 6.3 - - - +
88B ALA 2.9 29.7 + - - +
90B THR* 2.7 60.1 + - + +
91B SER 3.5 2.9 - - - +
92B GLU* 3.9 27.6 + - - +
96B LEU* 2.9 38.3 + - - +
98B GLY 3.7 3.9 + - - +
99B TRP* 1.3 81.1 - - - +
101B TRP* 1.3 68.4 + - - +
102B ILE* 3.6 4.8 + - + +
72D VAL* 6.1 3.8 - - + -
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Residues in contact with TRP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TRP* 3.3 21.1 - + + -
51A TYR* 3.1 63.9 + + - -
52A PHE* 4.0 2.9 - + - -
53A TYR* 3.8 15.5 - - + -
29B ASP* 3.2 5.4 - - - +
30B ILE* 2.9 48.9 + - + +
85B TYR* 3.8 19.7 - - + -
86B VAL* 3.3 30.3 - - - -
87B ARG* 3.3 46.9 - - + +
100B ARG* 1.3 72.5 - - - +
102B ILE* 1.3 59.0 + - - +
70D PRO* 3.5 21.3 - - + +
72D VAL* 6.4 0.2 - - + -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LYS* 4.8 2.2 - - + -
27B ALA* 4.0 27.4 - - + -
28B ILE 3.8 6.1 - - - +
29B ASP* 4.1 14.1 - - + -
35B VAL* 4.3 12.1 - - + -
37B VAL* 4.2 6.5 - - + -
52B PHE* 4.1 17.9 - - + -
84B THR 3.3 1.2 - - - +
85B TYR* 3.1 9.2 - - - -
86B VAL* 2.7 46.3 + - + +
88B ALA* 3.5 25.4 - - + -
90B THR* 4.7 2.2 - - + -
100B ARG* 4.0 9.2 - - + +
101B TRP* 1.3 79.1 - - - +
103B ARG* 1.3 60.6 + - - +
104B ILE* 3.6 16.4 + - + -
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 5.6 9.5 - - - +
24B LYS* 5.4 0.9 + - - -
27B ALA* 4.8 7.6 - - - +
28B ILE* 3.3 31.4 + - + +
29B ASP 4.8 0.9 - - - +
83B GLN* 3.7 47.6 + - + +
84B THR* 3.3 9.6 + - - +
85B TYR* 3.3 43.1 + - + -
102B ILE* 1.3 76.0 - - - +
104B ILE* 1.3 65.7 + - - +
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS* 3.6 27.4 - - + +
27B ALA* 5.9 0.2 - - + -
52B PHE* 4.2 19.7 - - + -
53B TYR 4.0 20.9 - - - +
54B GLU* 4.1 10.8 - - + -
83B GLN* 3.1 10.0 - - - +
84B THR* 2.9 35.8 + - + +
86B VAL* 3.7 30.3 - - + -
102B ILE* 3.6 23.3 + - + +
103B ARG* 1.3 79.5 - - - +
105B ASP* 1.3 64.7 + - - +
106B THR* 4.1 2.1 - - - -
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TYR 4.4 0.9 - - - +
54B GLU* 3.4 29.6 + - + +
55B THR 3.1 30.8 + - - +
56B ARG* 4.1 13.5 - - + +
81B THR* 3.5 24.0 - - + +
82B SER 3.7 5.2 - - - -
83B GLN* 3.0 25.0 + - - +
104B ILE* 1.3 75.1 - - - +
106B THR* 1.3 59.3 + - - +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 3.8 11.4 + - - +
106A THR* 2.8 42.3 + - - +
53B TYR 5.6 1.3 + - - -
54B GLU* 5.4 0.2 - - - +
55B THR* 3.2 23.9 + - - +
82B SER* 2.9 14.9 + - - +
83B GLN 4.0 2.2 - - - +
84B THR* 3.8 34.8 - - - +
104B ILE* 4.1 4.3 - - - -
105B ASP* 1.3 75.5 - - - +
107B SER* 1.3 75.9 + - - +
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A SER* 5.2 0.2 - - - -
107A SER* 3.3 37.4 - - - -
109A VAL* 4.9 2.9 - - - -
16B SER* 5.6 0.2 - - - -
55B THR* 3.3 18.2 + - - +
56B ARG* 4.4 0.3 - - - -
81B THR* 3.4 5.5 - - - +
82B SER* 2.6 47.4 + - - +
106B THR* 1.3 83.7 - - - +
108B CYS* 1.3 65.2 + - - +
109B VAL* 4.0 3.6 - - - +
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Residues in contact with CYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 3.7 15.6 - - - +
14B CYS* 3.7 31.3 - - + +
15B ASP 3.8 6.1 - - - -
16B SER* 3.8 18.0 - - - -
57B CYS* 2.0 58.3 - - - +
79B CYS* 3.7 4.5 - - - -
80B LYS 3.6 2.9 - - - -
107B SER* 1.3 75.9 - - - +
109B VAL* 1.3 65.1 + - - +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 6.6 0.2 - - - -
13A VAL* 6.3 0.2 - - + -
107A SER* 4.9 3.4 - - - -
108A CYS 3.7 23.3 - - - +
109A VAL* 4.3 6.7 - - + +
14B CYS* 4.0 5.6 - - - -
79B CYS* 3.5 1.0 - - - -
80B LYS* 2.8 51.1 + - + +
82B SER* 4.0 14.4 - - - +
107B SER* 4.0 16.4 - - - +
108B CYS* 1.3 79.0 - - - +
110B CYS* 1.3 67.3 + - - +
111B ALA* 3.8 2.0 + - + -
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Residues in contact with CYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 4.1 4.0 - - - -
13A VAL* 3.5 49.1 + - + +
13B VAL* 3.8 13.3 - - + +
14B CYS* 3.7 8.4 - - - +
67B CYS* 2.0 47.8 - - - -
70B ILE* 3.8 8.5 - - - -
77B SER* 4.0 7.4 - - - -
78B GLN 3.4 3.8 - - - -
109B VAL* 1.3 80.7 - - - +
111B ALA* 1.3 60.3 + - - +
112B LEU* 4.4 1.3 - - - -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 3.8 30.1 - - - +
11A TYR 3.6 6.5 - - - +
12A SER* 5.0 0.7 - - - +
77B SER* 3.3 5.1 - - - -
78B GLN* 2.9 33.6 + - + +
80B LYS* 4.2 18.8 - - + -
109B VAL* 3.8 1.8 + - + -
110B CYS* 1.3 75.4 - - - +
112B LEU* 1.3 63.7 + - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 2.7 33.1 - - - +
11A TYR* 2.6 30.3 + - + +
12A SER 4.7 1.6 - - - +
13A VAL* 3.7 17.7 - - + -
68A ARG* 3.7 22.9 - - + +
69A GLY* 3.6 25.8 - - - -
70B ILE* 3.8 29.4 - - + -
75B TRP* 4.1 29.2 - - + -
76B ASN 3.4 11.0 - - - +
77B SER* 4.1 5.4 - - - -
111B ALA* 1.3 74.3 - - - +
113B SER* 1.3 56.1 + - - +
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLY 3.8 17.7 - - - -
10A GLU* 4.3 6.1 - - - -
11A TYR* 4.8 1.3 - - - -
75B TRP* 3.5 10.2 - - - -
76B ASN* 2.8 59.8 + - - +
112B LEU* 1.3 75.5 - - - +
114B ARG* 1.3 61.3 + - - +
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLY 4.6 4.4 + - - -
11A TYR* 4.8 11.2 + - + -
74B HIS* 3.8 12.1 - - + +
75B TRP* 3.9 20.3 - - + -
76B ASN* 3.7 6.3 + - - -
113B SER* 1.3 78.8 + - - +
115B LYS* 1.3 71.6 + - - +
119D GLU* 3.1 24.0 + - - -
122D PRO* 5.0 8.5 - - - +
125D THR* 4.5 18.1 - - - +
135D PRO* 3.4 13.9 - - - +
136D CYS* 2.5 55.4 + - - +
138D PRO* 5.6 2.1 - - - +
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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
------------------------------------------------------------
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