Contacts of the strand formed by residues 67 - 72 (chain B) in PDB entry 3BN3
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 VAL 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A MET* 4.3 7.0 - - + -
203A LEU 4.2 8.3 - - - +
204A LEU* 4.7 6.3 - - + -
205A LEU* 3.9 22.7 - - + -
36B LEU* 3.4 3.5 - - - -
37B GLU* 2.8 44.0 + - + +
65B GLN 4.0 5.4 - - - +
66B PRO* 1.3 74.6 - - - +
68B CYS* 1.3 71.2 + - - +
69B PHE* 3.9 3.1 + - - -
78B GLN* 3.9 26.9 - - + +
79B ALA 3.7 7.2 - - - +
80B ARG* 3.2 30.3 - - + +
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Residues in contact with CYS 68 (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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5B ALA* 4.2 16.6 - - - -
6B ASP 3.9 13.5 - - - -
7B LEU* 3.9 9.6 - - + -
24B CYS* 2.0 53.6 - - + -
35B GLY 3.5 5.2 - - - -
36B LEU* 3.8 11.9 - - + +
66B PRO 4.0 0.6 - - - -
67B VAL* 1.3 73.9 - - - +
69B PHE* 1.3 59.8 + - - +
78B GLN* 3.1 8.5 - - - +
79B ALA* 2.7 39.4 + - - +
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Residues in contact with PHE 69 (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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205A LEU* 3.6 31.6 - - + -
243A THR* 3.6 48.7 - - + -
33B ARG* 4.8 7.9 - - + -
34B GLY* 3.3 10.4 - - - -
35B GLY* 2.9 68.2 + - - +
36B LEU 4.0 2.7 - - - -
37B GLU* 4.5 4.7 - - - -
67B VAL 4.0 4.0 - - - -
68B CYS* 1.3 76.7 - - - +
70B PHE* 1.3 77.0 + - - +
71B ARG* 4.8 1.8 - - + -
76B THR* 3.9 17.5 - - + -
77B LEU 3.2 11.0 - - - +
78B GLN* 4.2 2.5 - - + -
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Residues in contact with PHE 70 (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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5B ALA* 4.3 7.9 - - + -
24B CYS* 3.3 41.1 - - - -
25B SER 3.7 16.2 - - - -
26B THR* 3.7 29.4 - - + +
28B CYS* 5.5 0.4 - - + -
31B PRO* 3.9 25.6 - - + -
33B ARG 3.2 5.4 - - - +
34B GLY* 3.7 21.8 - - - -
35B GLY 5.2 0.2 - - - -
47B ARG* 5.5 4.3 - - - -
49B LEU 5.0 1.8 - - - -
50B ARG* 3.9 16.6 - - - -
51B TRP* 4.1 9.6 - - - -
52B LEU* 4.4 5.4 - - + -
69B PHE* 1.3 76.8 - - - +
71B ARG* 1.3 60.3 + - - +
76B THR* 3.5 4.7 - - - -
77B LEU* 2.7 44.9 + - + +
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Residues in contact with ARG 71 (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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31B PRO* 3.5 6.8 - - - +
32B GLU* 3.0 44.6 + - - +
33B ARG* 2.8 56.5 + - + +
69B PHE* 4.8 3.3 - - + -
70B PHE* 1.3 71.5 - - - +
72B CYS* 1.3 58.9 + - - +
73B ALA 3.7 8.2 + - - +
74B ARG* 3.4 30.9 + - - +
75B ARG 3.4 9.2 - - - -
76B THR* 3.2 27.5 + - + +
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Residues in contact with CYS 72 (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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3B PHE* 4.2 19.5 - - - -
28B CYS* 2.1 50.7 - - + -
29B PRO* 4.3 3.1 - - - -
32B GLU* 5.1 0.4 - - - -
70B PHE 3.6 0.4 + - - -
71B ARG* 1.3 73.4 - - - +
73B ALA* 1.3 75.6 + - - +
75B ARG* 2.6 28.9 + - + +
77B LEU* 3.5 29.2 - - + -
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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