Contacts of the strand formed by residues 67 - 74 (chain B) in PDB entry 2QV8
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 ARG 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B ARG* 3.7 14.6 - - - +
61B ILE* 3.5 3.5 - - - +
62B ASP* 2.8 54.4 + - + +
65B THR* 3.6 25.0 + - - +
66B ARG* 1.3 77.5 - - - +
68B LEU* 1.3 63.4 + - - +
69B THR* 4.1 1.6 - - - +
90B GLN* 3.6 36.9 + - + +
91B THR 3.3 13.7 - - - +
92B THR* 3.7 16.4 - - - +
99B LEU* 4.8 0.2 - - - +
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Residues in contact with LEU 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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35B SER* 5.8 0.2 - - - +
39B PHE* 3.7 33.4 - - + -
59B VAL* 4.7 2.5 - - + -
60B ARG 3.3 2.9 - - - -
61B ILE* 3.6 36.1 - - + -
66B ARG 5.1 1.3 - - - +
67B ARG* 1.3 77.9 - - - +
69B THR* 1.3 62.0 + - - +
70B PHE* 3.9 18.0 - - + -
90B GLN* 3.4 2.1 - - - +
91B THR* 2.8 51.7 + - + +
93B LEU* 4.9 12.3 - - + -
99B LEU* 4.3 13.0 - - + -
154B LEU* 4.4 13.7 - - + -
156B ILE* 5.3 2.0 - - + -
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Residues in contact with THR 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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58B GLY 3.8 0.3 - - - +
59B VAL* 3.3 6.3 - - - +
60B ARG* 2.9 57.4 + - - +
62B ASP* 4.5 1.7 + - - -
67B ARG* 4.4 4.7 + - - +
68B LEU* 1.3 76.9 - - - +
70B PHE* 1.3 65.3 + - - +
71B LEU* 3.7 24.4 + - + +
81B LYS* 3.9 15.0 - - + -
89B ASN 3.4 11.4 - - - +
90B GLN* 2.7 32.8 + - - +
136B GLU* 4.4 0.2 - - - +
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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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39B PHE* 3.8 29.8 - + - -
42B ARG* 3.9 38.6 - - + -
43B LEU* 4.5 5.8 - - - -
46B LEU* 4.4 13.7 - - + -
58B GLY 3.6 3.6 - - - +
59B VAL* 3.8 27.1 - - + -
68B LEU* 3.9 19.3 - - + -
69B THR* 1.3 70.8 - - - +
71B LEU* 1.3 60.7 + - - +
81B LYS* 3.6 4.0 - - - -
82B TRP* 2.9 24.4 + - + -
87B MSE 3.5 28.0 - - + -
88B THR 4.1 1.1 - - - -
89B ASN* 2.7 37.8 + - + +
91B THR* 4.0 9.0 - - - -
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Residues in contact with LEU 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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46B LEU* 4.6 0.5 - - - +
57B PHE* 3.3 12.5 - - - +
58B GLY 2.9 31.5 + - - +
60B ARG* 3.9 12.6 - - + +
69B THR* 3.7 29.2 - - + +
70B PHE* 1.3 75.2 - - - +
72B GLN* 1.3 60.5 + - - +
79B TRP* 3.9 16.4 - - + -
80B GLN 3.1 25.4 - - - +
81B LYS* 3.8 3.6 - - - +
82B TRP* 4.3 1.8 - - - -
136B GLU* 3.8 18.6 - - + +
137B PRO 3.6 22.4 - - - +
139B PRO* 3.7 29.8 - - + -
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Residues in contact with GLN 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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55B GLN* 4.5 15.7 - - + +
56B ASP 3.9 9.6 - - - +
57B PHE* 3.7 23.4 - - + -
71B LEU* 1.3 73.9 - - - +
73B LEU* 1.3 72.4 + - - +
74B THR* 3.5 19.1 + - + +
78B GLY 3.4 1.9 - - - +
79B TRP* 3.5 3.1 - - - -
80B GLN 2.7 35.5 + - - +
81B LYS 5.3 0.4 - - - +
82B TRP* 3.2 34.2 - - + +
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Residues in contact with LEU 73 (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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55B GLN* 4.9 6.6 - - - +
56B ASP* 3.2 31.9 + - + +
72B GLN* 1.3 80.7 - - - +
74B THR* 1.3 63.9 + - - +
75B ALA 4.4 0.2 + - - -
78B GLY* 3.6 26.9 - - - -
79B TRP* 3.4 45.7 - - + +
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Residues in contact with THR 74 (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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72B GLN* 3.8 24.9 - - + +
73B LEU* 1.3 83.5 - - - +
75B ALA* 1.3 58.4 + - - +
76B ASP* 3.6 11.4 - - - -
77B LYS* 3.0 25.0 + - + +
78B GLY* 2.7 49.1 + - - +
80B GLN* 4.3 13.2 - - + -
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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