Contacts of the helix formed by residues 113 - 120 (chain J) in PDB entry 1ZUM
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 PRO 113 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111J GLY 3.7 0.6 - - - -
112J LYS* 1.3 87.5 - - + +
114J TYR* 1.3 66.4 + - - +
115J VAL* 4.4 3.6 - - + +
116J ILE* 2.8 39.6 + - + +
117J SER* 2.9 10.6 + - - -
297J ASN* 5.9 1.8 - - - -
298J GLN* 3.5 13.9 - - - +
334J PRO* 3.5 12.6 - - + +
339J THR* 4.0 17.9 - - + +
340J GLU* 3.5 30.5 - - - +
341J GLN 4.6 0.7 - - - -
342J GLY 4.2 8.1 - - - +
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Residues in contact with TYR 114 (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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8J VAL* 3.3 26.5 - - + -
9J PRO 3.1 20.7 + - - -
11J PRO* 3.5 36.5 - - + +
100J THR* 3.6 23.6 - - - +
103J ALA* 3.8 12.8 - - + -
104J ALA* 3.8 31.9 - - - -
107J THR* 3.1 17.7 + - - +
112J LYS 3.3 0.2 + - - -
113J PRO* 1.3 71.6 - - - +
115J VAL* 1.3 69.0 + - + +
117J SER* 3.2 0.9 + - - -
118J TYR* 2.9 38.3 + + - +
334J PRO 2.9 17.3 + - - +
335J PHE* 3.9 19.3 - + + +
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Residues in contact with VAL 115 (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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8J VAL* 4.6 15.7 - - + -
113J PRO* 3.2 4.4 - - + +
114J TYR* 1.3 85.7 - - + +
116J ILE* 1.3 68.7 + - + +
118J TYR* 3.6 2.8 + - - +
119J LEU* 3.0 49.1 + - + +
334J PRO 4.8 0.6 + - - -
336J ASP 5.6 0.7 - - - +
337J SER* 4.5 30.5 - - - +
339J THR 5.8 2.2 - - - +
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Residues in contact with ILE 116 (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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112J LYS* 4.8 7.2 - - + +
113J PRO* 2.8 34.8 + - + +
115J VAL* 1.3 86.9 - - + +
117J SER* 1.3 59.9 + - - +
119J LEU* 6.1 0.4 - - + -
120J VAL* 2.8 46.9 + - + +
121J ASP* 3.2 19.3 + - - +
296J PHE* 4.0 28.5 - - + -
297J ASN* 6.0 1.8 - - - +
340J GLU 5.5 1.6 - - - +
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Residues in contact with SER 117 (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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103J ALA* 3.3 29.2 + - - -
106J GLU* 3.9 11.6 - - - +
107J THR* 3.0 18.4 + - - -
112J LYS* 3.2 20.8 - - - +
113J PRO 2.9 6.9 + - - -
114J TYR 3.6 6.1 - - - -
116J ILE* 1.3 75.3 - - - +
118J TYR* 1.3 58.3 + - - +
121J ASP* 3.5 11.6 + - - +
122J LEU* 2.9 36.4 + - - +
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Residues in contact with TYR 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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7J ALA 4.5 5.2 - - - -
8J VAL* 3.9 16.4 - - + -
9J PRO* 3.4 31.6 - - + +
99J ARG* 2.9 73.6 + - + +
100J THR* 3.6 21.7 + - - -
103J ALA* 3.7 10.5 - - + -
114J TYR* 2.9 34.5 + + + +
115J VAL 4.0 2.7 - - - +
117J SER* 1.3 80.8 - - - +
119J LEU* 1.3 77.4 + - + +
122J LEU* 3.9 5.8 - - - +
123J ASP 3.9 0.7 + - - -
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Residues in contact with LEU 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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7J ALA 4.4 11.2 - - - +
8J VAL* 3.7 26.0 - - + -
99J ARG* 4.1 5.5 + - - +
115J VAL* 3.0 33.7 + - + +
116J ILE* 5.1 0.4 - - + -
118J TYR* 1.3 93.4 - - + +
120J VAL* 1.3 66.7 + - + +
123J ASP* 3.2 20.4 - - - +
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Residues in contact with VAL 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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116J ILE* 2.8 42.5 + - + +
118J TYR 3.5 0.2 - - - -
119J LEU* 1.3 80.8 - - + +
121J ASP* 1.3 62.0 + - - +
122J LEU 3.5 0.2 - - - -
123J ASP* 3.3 2.2 + - - +
124J MET* 2.8 63.1 + - + +
296J PHE* 4.4 19.1 - - + -
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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
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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