Contacts of the strand formed by residues 102 - 106 (chain Q) in PDB entry 2WUB
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 THR 102 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6Q GLN* 3.9 8.6 + - - +
7Q SER 4.0 0.5 - - - -
8Q PRO* 2.5 33.6 + - + +
9Q SER 3.3 5.2 - - - -
10Q SER* 4.1 9.0 - - - -
11Q LEU* 4.3 5.6 - - + -
21Q ILE* 3.5 47.5 - - + +
84Q ALA 3.8 0.5 - - - +
85Q THR* 3.3 7.1 - - - +
86Q TYR* 2.8 31.8 + - - -
101Q GLY* 1.3 75.3 + - - -
103Q LYS* 1.3 66.2 + - - +
104Q VAL* 3.8 1.6 + - + -
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Residues in contact with LYS 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q SER 3.1 9.9 + - - +
10Q SER* 3.1 12.8 - - - -
11Q LEU 2.8 29.3 + - - +
84Q ALA* 3.8 6.7 - - - +
85Q THR* 3.9 19.5 - - + +
102Q THR* 1.3 72.0 - - - +
104Q VAL* 1.3 62.7 + - - +
105Q GLU* 3.6 35.3 + - + +
142Q ARG* 4.2 10.1 - - - +
165Q GLU* 3.0 39.3 + - - -
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Residues in contact with VAL 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q LEU* 3.5 26.9 - - + -
13Q ALA* 5.0 0.2 - - + -
19Q VAL* 4.4 8.3 - - + -
21Q ILE* 4.0 27.1 - - + -
75Q ILE* 5.8 2.2 - - + -
78Q LEU* 4.5 16.2 - - + -
82Q ASP 4.5 7.0 - - - +
83Q PHE* 3.2 32.2 - - + +
84Q ALA* 3.0 27.0 + - - +
86Q TYR* 4.0 15.7 - - + -
102Q THR* 4.5 1.1 - - + -
103Q LYS* 1.3 72.3 - - - +
105Q GLU* 1.3 61.2 + - - +
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Residues in contact with GLU 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q SER* 4.3 16.1 + - - -
11Q LEU 2.8 13.3 + - - +
12Q SER* 3.3 12.1 + - - +
13Q ALA 3.0 24.6 + - - -
83Q PHE* 3.2 12.4 - - - -
103Q LYS* 3.6 35.0 - - + +
104Q VAL* 1.3 74.1 - - - +
106Q ILE* 1.3 60.9 + - - +
142Q ARG* 2.9 30.6 + - - -
166Q GLN* 3.5 18.6 - - - +
173Q TYR* 3.3 12.1 + - - +
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Residues in contact with ILE 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q SER* 4.4 1.1 + - - -
13Q ALA 3.6 6.7 - - - +
14Q SER* 5.3 2.5 - - - -
15Q VAL* 5.8 3.6 - - + +
80Q PRO* 5.5 2.0 - - + +
83Q PHE* 3.5 40.8 - - + -
105Q GLU* 1.3 73.2 - - - +
107Q LYS* 1.3 72.6 + - - +
108Q ARG* 4.9 2.4 - - + +
140Q TYR* 3.0 15.9 + - - -
166Q GLN* 2.7 41.3 + - + +
167Q ASP 5.9 0.7 - - - +
171Q SER* 3.8 27.8 - - - +
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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