Contacts of the strand formed by residues 95 - 99 (chain B) in PDB entry 3GZN
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 GLN 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU 2.9 23.8 + - - +
68B ASP* 3.3 27.1 + - - +
69B THR* 4.5 2.9 - - - +
70B CYS 3.6 14.6 + - - +
71B LYS* 3.6 17.0 - - + -
72B VAL 3.0 24.9 + - - +
94B ARG* 1.3 92.3 - - - +
96B ILE* 1.3 59.2 + - - +
97B HIS* 4.4 8.1 - - + +
140B ASN* 3.1 31.7 + - - +
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.4 10.3 - - + +
74B VAL* 4.1 9.9 - - + -
85B LEU* 3.7 32.3 - - + +
88B LEU* 3.8 29.8 - - + -
89B ALA* 4.0 14.1 - - + +
93B PHE* 4.0 24.7 - - + +
94B ARG 3.2 7.7 + - - +
95B GLN* 1.3 78.3 - - - +
97B HIS* 1.3 75.6 + - - +
139B CYS* 4.6 10.1 - - - -
140B ASN 3.2 6.0 + - - +
141B VAL* 3.3 11.4 - - + -
142B VAL 2.8 24.4 + - - -
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Residues in contact with HIS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 4.9 15.2 - - + +
72B VAL 2.9 6.7 + - - -
73B LEU* 3.6 20.4 - - + -
74B VAL* 2.7 32.7 + - - +
95B GLN* 4.4 9.5 - - - +
96B ILE* 1.3 86.7 - - - +
98B VAL* 1.3 62.1 + - - +
142B VAL* 3.4 29.9 - - + +
144B HIS* 3.0 26.9 + + - +
155B PHE* 5.7 1.6 - + - -
158B GLN* 5.1 5.8 - - - -
159B PHE* 3.5 26.4 - + + -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 3.2 18.2 - - + +
76B GLY 4.9 3.8 - - - +
77B ALA* 5.0 5.8 - - + -
85B LEU* 3.3 42.2 - - + -
97B HIS* 1.3 77.2 - - - +
99B ILE* 1.3 64.9 + - - +
125B ALA* 4.2 19.4 - - + +
128B ALA* 5.5 0.7 - - + -
129B ALA* 4.7 0.4 - - + -
141B VAL* 4.0 13.5 - - + -
142B VAL 3.0 13.2 + - - +
143B PRO* 3.7 12.1 - - + -
144B HIS* 2.8 35.4 + - - +
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.7 36.1 - - + -
74B VAL 3.2 6.7 + - - +
75B ILE* 4.3 9.1 - - + +
76B GLY* 2.7 32.1 + - - -
98B VAL* 1.3 79.7 - - - +
100B ASP* 1.3 60.6 + - - +
144B HIS* 3.5 18.4 - - + +
146B ASN* 3.2 33.4 - - + +
147B LYS 4.3 0.7 - - - -
148B ILE* 4.1 19.3 - - + -
151B PHE* 4.2 6.5 - - + -
155B PHE* 3.9 16.6 - - + -
156B TYR* 4.0 16.6 - - + +
464I B39 4.3 2.1 + - + -
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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
------------------------------------------------------------
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