Contacts of the strand formed by residues 97 - 103 (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 LEU 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B GLU* 3.7 33.7 - - + +
32B ALA* 3.7 29.2 - - + +
35B SER* 3.9 19.7 - - - +
66B ARG* 3.4 24.6 + - - -
93B LEU* 4.2 13.5 - - + -
94B LYS* 3.0 29.6 + - + +
95B GLU 3.1 5.1 + - - +
96B GLY* 1.3 85.1 - - - +
98B GLN* 1.3 61.3 + - - +
156B ILE* 4.2 4.7 - - + -
157B PHE 3.4 16.2 - - - +
158B PRO* 4.2 4.5 - - + -
159B LYS* 4.3 3.5 - - - +
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Residues in contact with GLN 98 (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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66B ARG* 4.4 9.0 - - - +
93B LEU* 4.2 3.4 - - - -
97B LEU* 1.3 75.1 - - - +
99B LEU* 1.3 63.1 - - - +
156B ILE* 3.5 6.1 - - - +
157B PHE* 2.8 53.9 + - + +
159B LYS* 4.3 12.5 - - + +
160B GLY 5.8 0.2 - - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 3.7 25.8 - - + -
63B VAL* 3.6 36.3 - - + +
66B ARG* 4.0 29.1 - - + +
68B LEU* 4.3 19.7 - - + -
93B LEU* 3.5 27.1 - - + -
98B GLN* 1.3 77.7 - - - +
100B ASP* 1.3 64.5 + - - +
154B LEU* 3.8 13.5 - - + -
155B SER 3.1 13.0 - - - +
156B ILE* 4.4 3.4 - - + -
157B PHE* 4.1 5.3 - - - -
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Residues in contact with ASP 100 (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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63B VAL* 5.1 3.1 - - - -
99B LEU* 1.3 76.9 - - - +
101B PHE* 1.3 74.2 + - - +
102B GLU* 4.5 10.4 + - - +
153B THR 4.0 0.2 - - - +
154B LEU* 3.5 3.3 - - - +
155B SER* 2.8 38.7 + - - +
157B PHE* 3.8 20.2 - - + -
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Residues in contact with PHE 101 (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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61B ILE* 3.6 39.0 - - + -
63B VAL* 3.8 23.8 - - + +
99B LEU* 4.6 1.0 - - - +
100B ASP* 1.3 82.9 + - - +
102B GLU* 1.3 68.4 + - - +
103B LEU* 3.8 30.7 - - + -
140B GLN* 3.9 28.9 - - + -
141B LEU* 4.3 4.5 - - + -
152B PHE* 4.5 8.5 - + + -
153B THR 3.2 12.3 - - - +
154B LEU* 3.5 17.3 - - + -
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Residues in contact with GLU 102 (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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100B ASP* 4.8 9.0 - - - +
101B PHE* 1.3 78.0 - - - +
103B LEU* 1.3 68.0 + - - +
104B GLY* 6.2 0.2 - - - -
152B PHE* 3.3 5.4 - - - +
153B THR* 2.9 56.3 + - - +
155B SER* 5.6 1.2 + - - -
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Residues in contact with LEU 103 (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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101B PHE* 3.8 18.4 - - + -
102B GLU* 1.3 81.9 - - - +
104B GLY* 1.3 57.0 + - - +
140B GLN* 4.3 17.3 - - + +
141B LEU* 3.6 30.7 - - + -
150B THR* 3.9 11.4 - - + -
151B PRO 3.8 9.4 - - - +
152B PHE* 4.1 1.1 - - + -
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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
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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