Contacts of the strand formed by residues 80 - 84 (chain X) in PDB entry 2QW0
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 80 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54X GLN* 3.8 27.4 - - - +
55X GLN 2.9 13.3 + - - +
56X ARG* 3.4 11.4 - - + +
57X VAL* 3.0 23.3 + - - -
78X GLY 4.3 2.5 - - - +
79X ALA* 1.3 75.2 - - - +
81X PRO* 1.3 64.9 - - - +
82X ALA* 3.4 1.4 + - - +
155X PRO* 3.7 29.8 - - + +
156X ALA 3.6 23.3 - - - +
157X PHE* 3.9 1.8 - - - +
158X ILE* 3.9 29.8 - - + -
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Residues in contact with PRO 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X VAL 3.4 7.0 - - - +
59X VAL* 4.4 0.7 - - + -
71X ILE* 4.0 10.8 - - + +
74X LEU* 4.0 32.1 - - + -
75X HIS* 4.3 2.5 - - - +
79X ALA 3.4 7.0 - - - +
80X VAL* 1.3 82.4 - - - +
82X ALA* 1.3 55.1 + - - +
83X LEU* 3.8 21.5 + - + +
156X ALA 3.2 17.3 - - - +
157X PHE* 3.4 27.9 - - + +
158X ILE 2.7 32.1 + - - +
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Residues in contact with ALA 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X VAL 2.8 14.2 + - - +
58X ALA* 3.4 2.3 - - + -
59X VAL 2.8 25.4 + - - +
80X VAL 4.5 0.7 - - - +
81X PRO* 1.3 71.4 - - - +
83X LEU* 1.3 62.4 + - - +
84X LEU* 3.7 4.6 + - + +
102X MET* 4.0 22.2 - - + -
158X ILE* 3.3 23.8 - - + -
160X TYR* 3.8 20.9 - - + +
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Residues in contact with LEU 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X VAL* 3.6 34.3 - - + +
71X ILE* 3.7 28.5 - - + -
81X PRO* 3.9 16.2 - - + +
82X ALA* 1.3 70.5 - - - +
84X LEU* 1.3 61.2 + - - +
85X ASN 4.3 0.2 + - - -
157X PHE* 5.4 1.8 - - + -
158X ILE 3.0 14.8 + - - +
159X PHE* 3.5 25.1 - - + -
160X TYR* 3.4 19.8 + - - +
205X LEU 3.3 21.8 - - - +
206X TYR* 3.8 27.0 - - + +
211X PHE* 4.5 9.4 - - + -
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Residues in contact with LEU 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X ALA* 4.1 10.8 - - + -
59X VAL 2.9 15.9 + - - +
60X VAL* 4.0 23.9 - - + -
61X ALA 4.5 1.4 + - - +
82X ALA* 4.1 4.5 - - + +
83X LEU* 1.3 76.5 - - - +
85X ASN* 1.3 65.3 + - - +
86X PRO* 3.2 8.7 - - - +
88X LEU* 4.4 7.9 - - + -
93X LEU* 3.8 16.6 - - + -
96X LEU* 3.9 25.4 - - + -
97X ILE* 4.1 25.1 - - + -
102X MET* 5.5 0.4 - - - -
160X TYR* 3.4 44.9 - - + +
206X TYR* 3.9 7.1 - - - +
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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