Contacts of the strand formed by residues 71 - 75 (chain B) in PDB entry 4QGC
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 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B GLY* 6.5 0.2 - - - -
47B ILE 3.1 3.4 + - - -
48B ILE* 3.5 33.2 - - + -
49B CYS 2.9 27.0 + - - -
69B MET* 3.7 7.9 - - - +
70B ASN* 1.3 85.8 - - + +
72B ALA* 1.3 63.0 + - - +
108B VAL* 4.9 0.2 - - - -
109B ALA* 3.5 26.9 - - + +
111B ALA* 3.8 27.6 - - + -
239B MET* 4.2 15.0 - - + -
358B CYS* 5.9 0.7 - - - -
464B HIS* 4.2 18.4 - - + -
465B LEU* 5.4 2.2 - - + -
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Residues in contact with ALA 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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49B CYS 3.5 4.3 - - - -
51B ILE* 3.8 22.2 - - + -
69B MET* 4.5 7.4 - - - -
71B VAL* 1.3 72.8 - - - +
73B ARG* 1.3 60.7 + - - +
74B LEU* 3.9 3.6 + - + +
91B VAL* 4.0 28.3 - - + -
108B VAL* 4.5 1.9 - - + +
109B ALA 2.8 16.2 + - - +
110B VAL* 3.6 6.4 - - + +
111B ALA 2.8 28.0 + - - +
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Residues in contact with ARG 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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48B ILE* 4.1 13.7 - - + -
49B CYS 2.7 16.2 + - - +
50B THR* 2.6 47.5 + - - +
51B ILE* 3.0 26.0 + - - +
71B VAL 3.8 0.6 + - - -
72B ALA* 1.3 72.5 - - - +
74B LEU* 1.3 65.9 + - - +
75B ASN* 4.3 20.7 - - - +
111B ALA* 3.6 5.8 - - - +
113B ASP* 2.6 53.1 + - + +
241B PHE* 3.8 16.2 - - + -
270B LYS* 4.8 3.2 - - - +
360B MET* 3.4 37.6 - - - +
362B SER* 3.9 11.1 + - - -
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Residues in contact with LEU 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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51B ILE* 4.0 17.3 - - + +
72B ALA* 4.7 6.3 - - + +
73B ARG* 1.3 79.9 - - - +
75B ASN* 1.3 60.7 + - - +
76B PHE* 3.3 21.6 + - + -
84B HIS* 3.7 31.9 - - + +
87B THR* 3.6 26.7 - - + -
88B ILE* 3.5 34.1 - - + -
91B VAL* 5.3 2.5 - - + -
110B VAL* 4.8 8.3 - - + -
111B ALA 2.9 17.0 + - - +
112B LEU* 5.0 0.2 - - - -
113B ASP* 2.9 30.8 + - - +
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Residues in contact with ASN 75 (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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50B THR* 4.6 9.2 - - + +
51B ILE 5.1 2.8 + - - +
73B ARG* 3.9 28.2 + - - +
74B LEU* 1.3 70.0 - - - +
76B PHE* 1.3 59.2 + - - +
77B SER* 3.1 19.5 + - - -
78B HIS* 3.2 38.3 + - + +
84B HIS* 3.4 8.4 - - - -
113B ASP* 4.1 4.7 - - - -
1001B K 2.8 27.0 - - - -
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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