Contacts of the helix formed by residues 117 - 124 (chain J) 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 GLU 117 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58J HIS* 3.7 31.2 - - + +
113J GLU* 3.6 25.7 - - - +
114J GLN* 6.3 0.2 - - - +
115J ALA 2.9 2.2 + - - -
116J LYS* 1.3 82.5 - - - +
118J ALA* 1.3 60.3 + - - +
119J PHE 2.8 5.4 - - - +
120J ARG* 2.9 53.8 + - - +
121J LEU* 2.7 49.2 + - + +
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Residues in contact with ALA 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J MET* 2.7 44.0 - - + +
58J HIS* 4.4 11.9 - - + -
59J PHE* 3.4 39.7 - - + -
107J VAL* 4.7 0.4 - - + -
114J GLN 4.4 0.2 - - - +
115J ALA* 3.5 10.4 + - - +
117J GLU* 1.3 79.3 - - - +
119J PHE* 1.3 61.9 - - + +
121J LEU* 4.5 3.6 - - - +
122J ALA* 3.5 9.4 + - - +
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Residues in contact with PHE 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J TYR 4.4 0.4 - - - -
34J GLY* 2.9 30.3 - - - -
35J LEU* 3.1 28.8 - - + +
55J MET* 3.5 21.3 - - - -
105J PHE* 3.7 8.3 - - + -
106J GLU 3.3 23.6 - - - -
107J VAL* 3.5 37.2 - - + -
115J ALA 3.5 8.4 + - - +
116J LYS* 5.3 0.2 - - - -
117J GLU 2.8 1.4 - - - +
118J ALA* 1.3 78.0 - - - +
120J ARG* 1.3 68.8 + - - +
121J LEU 3.1 1.1 - - - -
122J ALA* 2.8 6.0 + - - -
123J GLY* 2.6 24.7 + - - -
132J MET* 3.0 36.1 - - + -
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Residues in contact with ARG 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84 LYS* 6.4 0.4 - - - -
116J LYS 4.5 4.9 - - - +
117J GLU* 2.9 52.7 + - - +
119J PHE* 1.3 78.9 - - - +
121J LEU* 1.3 84.8 + - - +
123J GLY* 3.0 6.9 + - - -
124J HIS* 3.2 28.6 + - + -
2446X C 3.9 2.6 + - - -
2447X G 2.5 32.9 + - - -
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Residues in contact with LEU 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J VAL* 3.5 24.7 - - + +
58J HIS* 4.8 19.1 - - + +
117J GLU* 2.7 45.1 + - + +
118J ALA* 4.5 1.6 - - - +
120J ARG* 1.3 87.3 - - - +
122J ALA* 1.3 54.3 + - - +
124J HIS* 2.4 45.9 + - - +
125J LYS* 3.2 6.7 - - - +
2446X C 4.5 7.6 - - - +
2447X G 4.3 20.9 - - - -
2448X A 6.0 4.7 - - - -
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Residues in contact with ALA 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J LEU* 5.0 7.6 - - + -
51J CYS* 3.7 23.5 - - + +
54J VAL* 3.9 5.0 - - - +
55J MET* 4.2 13.7 - - + -
105J PHE* 5.0 0.9 - - + -
118J ALA 3.5 15.9 + - - +
119J PHE* 2.8 13.2 + - - +
121J LEU* 1.3 74.6 - - - +
123J GLY* 1.3 65.3 + - - +
125J LYS* 2.7 32.1 + - - +
126J LEU* 3.6 8.2 + - - +
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Residues in contact with GLY 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J LEU* 5.0 2.8 - - - +
119J PHE 2.6 17.1 + - - -
120J ARG* 3.4 5.8 - - - -
121J LEU 2.6 2.0 + - - -
122J ALA* 1.3 71.5 - - - +
124J HIS* 1.3 51.0 + - - -
125J LYS 2.7 0.9 + - - -
126J LEU* 2.7 45.6 + - - +
128J ILE 4.9 3.4 - - - +
130J THR* 4.9 11.4 - - - -
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Residues in contact with HIS 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J ARG* 3.2 41.5 + - + -
121J LEU* 2.4 26.2 + - - +
123J GLY* 1.3 64.9 - - - -
125J LYS* 1.3 61.7 + - + -
126J LEU 3.5 1.6 - - - -
1040X A 6.1 0.7 - - - -
1041X G 4.8 20.3 + - - -
1042X G 5.7 2.0 + - - -
2445X C 3.7 15.5 + - + +
2446X C 3.3 61.6 + - - +
2463X G 2.8 26.2 + - - -
2464X G 4.2 4.7 + - - -
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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