Contacts of the strand formed by residues 81 - 94 (chain B) in PDB entry 3B4V
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 CYS 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A LEU* 5.7 1.6 - - - +
78A LYS 5.8 0.2 - - - +
116A SER* 5.4 0.7 - - - -
11B CYS* 2.0 56.5 - - + -
12B CYS 3.8 2.0 - - - -
40B CYS* 3.8 17.8 - - - +
41B GLU* 3.6 25.4 - - - -
42B GLY 3.6 23.5 + - - +
44B CYS* 3.5 4.6 - - - -
79B SER 4.3 0.2 + - - -
80B CYS* 1.3 73.1 - - - +
82B VAL* 1.3 63.5 + - - +
113B CYS* 4.4 0.2 - - - -
114B GLY 3.7 0.4 - - - -
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Residues in contact with VAL 82 (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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80A CYS* 4.9 0.2 - - - -
82A VAL* 3.5 41.5 - - + -
83A PRO* 5.4 2.0 - - + +
116A SER* 3.5 25.6 - - - +
40B CYS* 3.3 7.4 - - - -
80B CYS* 3.8 17.3 - - + +
81B CYS* 1.3 80.5 - - - +
83B PRO* 1.3 80.9 - - + +
84B THR* 3.4 3.3 + - + -
113B CYS* 3.3 2.1 - - - -
114B GLY 3.0 36.6 + - - +
115B CYS 4.9 0.2 - - - -
116B SER* 4.2 7.6 - - - +
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Residues in contact with PRO 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 4.5 9.4 - - + +
60A SER* 6.1 0.4 - - - +
82A VAL* 5.2 1.7 - - + +
83A PRO 4.1 12.0 - - - +
84A THR* 5.5 1.9 - - - +
116A SER* 4.1 19.3 - - - +
40B CYS* 3.3 10.7 - - + +
82B VAL* 1.3 97.7 - - + +
84B THR* 1.3 60.8 + - - +
85B LYS 4.6 1.1 - - - +
86B LEU* 4.0 28.9 - - + -
110B VAL* 3.8 24.7 - - + -
112B GLU 3.4 7.9 - - - +
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Residues in contact with THR 84 (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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83A PRO 5.4 4.3 - - - +
84A THR* 4.8 11.6 - - - +
85A LYS* 6.1 0.2 - - - -
86A LEU* 5.7 11.6 - - + +
57B SER* 6.2 3.6 - - - -
82B VAL* 3.4 4.2 + - + +
83B PRO* 1.3 76.3 - - - +
85B LYS* 1.3 60.5 + - - +
86B LEU* 6.1 0.2 - - - -
112B GLU* 2.8 29.5 + - - +
113B CYS 3.8 4.0 + - - -
114B GLY* 3.9 27.1 - - - +
115B CYS 5.4 3.4 - - - +
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Residues in contact with LYS 85 (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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83B PRO* 3.6 0.7 - - - +
84B THR* 1.3 83.0 + - - +
86B LEU* 1.3 69.6 + - - +
87B ARG* 5.9 0.4 - - + -
110B VAL* 3.6 5.0 - - - +
111B GLU* 2.7 44.3 + - + -
112B GLU* 3.3 42.9 + - + +
178G SER 5.4 4.3 - - - +
179G SER* 5.4 3.8 - - - +
180G PRO* 3.8 34.4 - - - +
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Residues in contact with LEU 86 (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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57A SER* 4.5 11.7 - - - +
59A HIS* 4.1 14.4 - - + +
84A THR* 5.9 8.3 - - + -
83B PRO* 4.0 16.4 - - + -
84B THR 6.1 0.2 - - - -
85B LYS* 1.3 86.5 - - - +
87B ARG* 1.3 63.4 + - - +
107B ASN* 4.0 42.4 - - + +
109B ILE 3.1 19.5 - - - +
110B VAL* 3.6 28.9 - - + +
111B GLU* 4.3 1.1 - - - +
178G SER* 5.9 4.0 - - - -
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Residues in contact with ARG 87 (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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85B LYS* 5.9 0.7 - - + -
86B LEU* 1.3 78.1 - - - +
88B PRO* 1.3 81.4 + - + +
106B GLN* 5.3 0.7 - - - -
107B ASN 4.2 5.4 - - - +
108B MET 3.2 19.1 + - - -
109B ILE* 2.9 56.3 + - + +
111B GLU* 2.7 44.7 + - + +
129C GLY* 3.1 30.4 + - - -
130C HIS* 3.5 28.1 + - - +
131C PRO* 5.0 4.0 - - - +
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Residues in contact with PRO 88 (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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87B ARG* 1.3 106.9 + - + +
89B MET* 1.3 63.7 + - - +
104B ASP* 4.5 15.7 - - + +
105B ILE 3.2 17.0 - - - +
106B GLN* 3.4 41.2 - - - +
108B MET* 4.6 0.2 - - - -
109B ILE* 4.0 4.7 - - - +
179G SER* 6.2 4.7 - - - -
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Residues in contact with MET 89 (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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32B PRO* 4.5 17.3 - - + -
35B TYR* 3.7 43.3 - - + -
88B PRO* 1.3 76.4 - - - +
90B SER* 1.3 73.1 + - - +
91B MET* 3.6 1.4 + - - +
104B ASP* 4.1 4.9 - - - -
105B ILE* 2.7 35.1 + - - +
108B MET* 3.7 21.5 - - + -
109B ILE* 4.2 13.7 - - + -
132C ASP* 4.1 22.0 - - + +
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Residues in contact with SER 90 (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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32B PRO* 4.3 9.0 - - - +
89B MET* 1.3 83.8 - - - +
91B MET* 1.3 64.2 + - - +
102B LYS* 3.5 33.3 - - - +
103B LYS 3.7 1.1 - - - -
104B ASP* 3.5 19.9 + - - -
111C SER 5.9 0.9 - - - -
112C ASP* 4.9 13.9 + - - -
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Residues in contact with MET 91 (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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58A PHE* 3.9 25.8 - - + -
20B PHE* 4.0 8.1 - - + -
29B ILE* 3.6 35.7 - - + -
31B ALA 3.9 2.7 - - - +
32B PRO* 3.9 21.3 - - - -
89B MET* 4.0 0.7 - - - +
90B SER* 1.3 80.3 + - - +
92B LEU* 1.3 60.3 + - - +
93B TYR* 3.8 8.8 - - + -
101B ILE 3.4 1.9 - - - +
102B LYS* 3.2 6.4 - - - +
103B LYS 2.8 38.0 + - - +
105B ILE* 3.9 21.8 - - + -
108B MET* 3.8 26.7 - - + -
61D LEU* 4.6 7.0 - - + -
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Residues in contact with LEU 92 (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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29B ILE* 3.6 3.5 - - - +
30B ILE* 2.8 53.6 + - + -
31B ALA* 2.8 26.9 + - + +
91B MET* 1.3 72.1 - - - +
93B TYR* 1.3 57.7 + - - +
100B ILE* 3.5 26.9 - - + -
101B ILE 3.2 13.5 - - - +
102B LYS* 4.0 7.0 - - + -
157C VAL* 4.0 9.9 - - + -
159C ASP* 3.9 12.8 - - + -
165C HIS* 3.9 30.3 - - + +
167C VAL* 3.8 17.0 - - + -
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Residues in contact with TYR 93 (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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28B TRP 3.2 17.0 - - - +
29B ILE* 4.2 5.8 - - + -
30B ILE* 3.9 9.9 - - - +
91B MET* 3.8 15.0 - - + -
92B LEU* 1.3 75.9 - - - +
94B TYR* 1.3 73.8 + - - +
99B ASN 3.2 1.9 - - - +
100B ILE* 3.7 1.0 - - - -
101B ILE* 2.8 73.6 + - + +
103B LYS* 3.5 38.3 + - + +
105B ILE* 4.2 6.1 - - + -
61D LEU* 3.5 60.8 + - + -
63D LEU* 4.4 9.8 - - + +
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Residues in contact with TYR 94 (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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27B ASP 3.4 24.0 - - - -
28B TRP* 2.9 21.9 + - + +
30B ILE* 3.3 34.4 - - + +
93B TYR* 1.3 84.5 - - - +
95B ASP* 1.3 63.2 + - - +
98B GLN* 3.6 37.7 - - - +
99B ASN 3.3 4.9 - - - -
100B ILE* 4.4 3.1 - - + +
199C ARG* 3.1 56.5 + - + +
202C THR* 4.3 14.1 - - + -
203C CYS* 3.5 16.6 - - - +
61D LEU* 4.9 1.4 - - - +
63D LEU* 3.6 9.4 - - - +
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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