Contacts of the helix formed by residues 95 - 101 (chain B) in PDB entry 2GZD
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 LYS 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ASP* 3.2 27.3 + - + +
93B ILE 3.2 4.4 + - - -
94B ALA* 1.3 85.7 + - + +
96B HIS* 1.3 65.5 + - - +
97B LEU* 3.2 8.6 + - + +
98B THR* 2.8 41.1 + - + +
99B TYR 3.7 2.3 + - - -
133B ALA* 4.3 0.2 - - - -
134B VAL* 4.1 2.3 - - - +
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Residues in contact with HIS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LYS* 1.3 72.3 - - - +
97B LEU* 1.3 57.5 + - - +
99B TYR* 3.1 24.3 + + - +
100B GLU* 2.7 61.9 + - + +
133B ALA* 3.6 30.1 - - + +
134B VAL* 4.1 15.3 - - + -
135B PRO* 5.3 2.2 - - + -
138B GLU* 4.6 11.0 + - - -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASP* 4.7 2.5 - - - +
95B LYS* 3.2 7.1 - - + -
96B HIS* 1.3 79.4 - - - +
98B THR* 1.3 59.0 + - + +
100B GLU* 3.3 24.7 + - + +
101B ASN* 2.9 57.9 + - - +
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASP* 3.5 27.8 + - + +
20B SER 4.8 4.9 - - - +
21B GLY 6.0 0.2 - - - -
22B VAL* 3.6 29.8 - - + -
90B VAL 4.9 1.9 - - - +
91B TYR* 3.5 11.6 - - - +
92B ASP* 3.1 23.4 + - + -
95B LYS* 2.8 36.8 + - + +
97B LEU* 1.3 78.0 - - + +
99B TYR* 1.3 58.4 + - - +
101B ASN* 3.8 4.5 + - - +
102B VAL* 3.8 14.0 + - - +
105B TRP* 5.2 2.1 - - - -
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Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 3.9 29.6 - + + +
96B HIS* 3.1 26.6 + + - +
98B THR* 1.3 78.1 + - - +
100B GLU* 1.3 65.8 + - - +
102B VAL* 3.1 27.1 + - + +
103B GLU 4.8 0.2 + - - -
121B LEU* 4.6 8.5 - - + -
134B VAL* 3.7 30.3 - - + -
138B GLU* 3.5 31.1 + - - +
139B ALA* 3.3 30.5 + - + -
142B PHE* 3.3 35.8 - + + +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B HIS* 2.7 54.8 + - + +
97B LEU* 3.4 26.5 + - + +
99B TYR* 1.3 74.6 - - - +
101B ASN* 1.3 60.7 + - - +
102B VAL 3.1 5.1 + - - -
103B GLU* 3.8 20.3 + - - +
104B ARG* 5.0 1.2 + - - +
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Residues in contact with ASN 101 (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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19B ASP* 2.8 41.5 + - - +
70B LEU* 4.5 9.8 - - + +
97B LEU* 2.9 38.2 + - - +
98B THR 4.1 1.6 - - - +
99B TYR 3.3 0.4 - - - -
100B GLU* 1.3 75.5 - - - +
102B VAL* 1.3 64.2 + - - +
103B GLU 3.3 1.1 - - - -
104B ARG* 3.0 41.9 + - + +
105B TRP* 3.2 15.8 - - - +
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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
------------------------------------------------------------
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