Contacts of the strand formed by residues 89 - 95 (chain B) in PDB entry 2QNU
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 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B PHE* 4.2 21.8 - - + -
7B TYR 3.7 10.3 - - - +
8B GLY 4.5 0.7 - - - -
9B MLZ 3.5 29.4 - - - +
10B LEU* 4.2 11.7 - - + -
17B VAL* 5.0 0.2 - - + -
76B VAL* 3.5 1.6 - - - -
77B MSE 2.9 37.5 + - + +
79B SER* 3.7 7.3 - - - -
88B PRO* 1.3 73.4 - - - +
90B THR* 1.3 66.1 + - - +
119B LEU* 3.6 28.4 - - + +
122B THR* 3.8 33.0 - - + +
132B PHE* 4.2 7.2 - - + -
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Residues in contact with THR 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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6B PHE* 3.1 8.0 - - - +
7B TYR* 2.9 38.2 + - - -
21B LEU* 6.2 0.7 - - + -
25B PHE* 5.1 1.1 - - + -
29B TRP* 3.1 48.1 + - + +
33B LEU* 4.4 3.6 - - - +
60B PHE* 3.8 18.2 - - + -
75B VAL 3.5 11.7 - - - +
76B VAL* 3.5 9.5 - - + +
88B PRO 4.8 0.2 - - - -
89B LEU* 1.3 78.4 + - - +
91B VAL* 1.3 70.2 + - - +
92B ALA* 4.1 7.4 - - + -
119B LEU* 4.5 0.2 - - - -
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Residues in contact with VAL 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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4B VAL* 3.5 25.8 - - + -
5B GLY 3.4 7.2 - - - +
6B PHE* 4.1 4.5 - - + -
74B GLY* 3.2 4.8 - - - -
75B VAL 3.0 31.3 + - - +
90B THR* 1.3 75.6 - - - +
92B ALA* 1.3 63.1 + - - +
111B TRP* 5.3 0.9 - - + -
115B VAL* 3.7 30.7 - - + +
118B LEU* 5.6 1.8 - - + -
119B LEU* 3.6 26.6 - - + +
132B PHE* 4.0 20.9 - - + -
136B VAL* 4.3 8.3 - - + -
139B LEU* 4.4 6.1 - - + -
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Residues in contact with ALA 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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3B SER 4.5 0.2 - - - +
4B VAL* 3.6 4.2 - - - +
5B GLY 3.0 32.3 + - - -
21B LEU* 3.4 16.7 - - + +
25B PHE* 4.2 21.8 - - + -
60B PHE* 4.6 1.8 - - + -
72B VAL* 3.9 22.0 - - + -
73B THR 3.4 4.9 - - - +
74B GLY* 4.4 0.2 - - - -
90B THR* 4.1 8.2 - - + -
91B VAL* 1.3 75.1 - - - +
93B CYS* 1.3 61.0 - - - +
94B LEU* 4.1 0.9 - - + -
111B TRP* 5.2 0.2 - - - -
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Residues in contact with CYS 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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3B SER* 3.7 26.2 - - - +
4B VAL* 4.2 6.5 - - + -
72B VAL* 3.6 3.1 - - - -
73B THR* 2.8 39.1 + - + +
92B ALA* 1.3 73.2 - - - +
94B LEU* 1.3 73.7 + - - +
95B LEU* 3.6 10.4 + - - +
111B TRP* 4.0 22.5 - - + -
141B ALA* 4.4 4.0 - - - -
142B PRO* 3.7 23.1 - - + -
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Residues in contact with LEU 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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3B SER* 4.2 7.8 + - - +
21B LEU* 4.6 11.6 - - + +
22B PRO* 3.8 32.3 - - + -
24B THR* 4.6 3.8 - - - +
25B PHE* 3.9 35.2 - - + -
70B GLU* 3.2 40.8 - - + +
71B ALA 3.4 5.8 - - - +
72B VAL* 4.6 7.0 - - + +
92B ALA* 4.1 0.8 + - + -
93B CYS* 1.3 83.3 - - - +
95B LEU* 1.3 59.8 + - - +
96B PRO* 4.7 0.9 - - - +
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Residues in contact with LEU 95 (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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70B GLU* 3.1 24.6 - - - +
71B ALA* 2.7 20.8 + - + +
73B THR* 3.9 26.0 - - + +
93B CYS* 4.1 21.3 - - - +
94B LEU* 1.3 75.5 - - - +
96B PRO* 1.3 80.5 - - + +
99B ALA* 3.8 13.9 - - + -
101B LEU* 3.9 26.7 - - + -
104B LEU* 3.9 7.2 - - + -
141B ALA* 5.2 4.3 - - + -
142B PRO* 4.5 7.0 - - + -
144B CYS* 4.1 25.1 - - + -
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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