Contacts of the helix formed by residues 93 - 99 (chain I) in PDB entry 2ZJQ
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 LEU 93 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87I THR* 3.1 21.8 - - - +
88I PHE* 2.9 27.4 - - + +
89I ASP 4.1 2.8 + - - +
90I ARG* 2.9 36.7 - - - +
92I THR* 1.3 79.9 - - + +
94I GLU* 1.3 51.7 + - - +
95I ALA* 3.2 1.8 - - - -
96I TYR* 3.7 13.1 + - + +
97I ARG* 2.6 34.1 + - + +
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Residues in contact with GLU 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88I PHE 3.8 0.4 + - - -
89I ASP* 3.5 18.0 - - - +
90I ARG 4.5 0.9 + - - -
91I ASP* 2.9 33.7 - - - +
92I THR 2.2 30.0 + - - +
93I LEU* 1.3 67.4 - - - +
95I ALA* 1.3 67.1 + - - +
97I ARG* 2.7 40.7 + - - +
98I LEU 2.9 8.5 + - - -
99I VAL* 2.7 26.0 - - + +
106I VAL* 4.9 19.0 - - - +
121I HIS 5.4 0.7 - - - +
122I VAL* 5.2 10.6 + - - +
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Residues in contact with ALA 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I THR* 2.5 24.8 + - + +
94I GLU* 1.3 68.0 - - - +
96I TYR* 1.3 71.2 + - + +
98I LEU* 2.4 33.1 + - - -
99I VAL* 3.6 4.9 + - - +
100I ARG* 4.3 22.1 - - + +
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Residues in contact with TYR 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I THR* 6.4 1.6 - - + -
93I LEU* 3.7 14.4 + - + +
95I ALA* 1.3 80.8 - - + +
97I ARG* 1.3 65.9 + - - +
98I LEU* 2.8 4.8 + - - +
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Residues in contact with ARG 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I VAL* 4.3 14.5 - - - +
79I GLN* 4.7 6.7 + - - +
80I LEU* 4.7 16.7 - - - +
84I GLU* 3.7 28.8 + - - +
87I THR* 3.2 30.7 - - - +
88I PHE 3.4 16.7 + - - -
89I ASP* 4.2 10.5 + - - +
93I LEU* 2.6 22.6 + - + +
94I GLU* 2.7 49.7 + - - +
95I ALA 2.9 0.8 + - - -
96I TYR* 1.3 77.6 - - - +
98I LEU* 1.3 68.1 + - - +
99I VAL* 3.5 21.4 - - - +
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Residues in contact with LEU 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I GLN* 5.6 1.4 - - - +
94I GLU 2.9 1.0 + - - -
95I ALA 2.4 20.5 + - - -
96I TYR 2.8 3.5 - - - +
97I ARG* 1.3 78.9 + - - +
99I VAL* 1.3 78.0 + - - +
100I ARG* 4.2 18.4 - - + +
613X A 4.0 2.5 - - - +
614X G 3.3 71.3 - - + +
636X G 4.4 13.7 - - - +
637X G 5.6 2.0 - - - +
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Residues in contact with VAL 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I GLU* 5.4 3.1 - - - +
74I VAL 5.5 2.2 - - - +
75I VAL* 4.1 35.9 - - + +
79I GLN* 5.3 9.4 - - + +
94I GLU* 2.7 49.8 - - + +
95I ALA* 3.6 1.3 + - - +
97I ARG* 3.5 13.0 - - - +
98I LEU* 1.3 82.5 - - - +
100I ARG* 1.3 64.8 - - - +
101I ARG* 3.4 7.8 + - - +
106I VAL* 6.0 1.6 - - - +
637X G 3.7 19.2 + - - +
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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