Contacts of the helix formed by residues 79 - 87 (chain J) in PDB entry 1N34
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 ARG 79 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77J PRO 2.6 10.7 + - - -
78J ASN* 1.3 68.8 - - - +
80J LYS* 1.3 52.3 + - - +
81J THR 2.8 2.0 - - - -
82J ILE* 2.7 33.5 + - - +
83J GLU* 2.5 24.1 - - - +
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Residues in contact with LYS 80 (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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30J SER* 3.7 36.5 + - - +
78J ASN* 2.5 11.9 + - - +
79J ARG* 1.3 75.6 - - - +
81J THR* 1.3 58.9 + - - +
82J ILE 2.9 4.9 + - - -
83J GLU* 3.1 19.8 + - + +
84J GLN* 3.4 17.8 + - + +
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Residues in contact with THR 81 (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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27J ALA* 2.9 28.8 - - - +
30J SER* 2.8 19.0 + - - +
31J GLY* 2.8 38.2 + - - +
32J ALA 3.8 8.3 - - - +
74J ILE* 4.4 1.8 - - + +
77J PRO* 3.4 16.5 - - + +
78J ASN* 2.8 25.5 + - - +
79J ARG 2.8 0.8 + - - -
80J LYS* 1.3 77.0 + - - +
82J ILE* 1.3 64.6 + - - +
84J GLN* 3.1 7.2 - - - +
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Residues in contact with ILE 82 (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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4J ILE* 4.4 15.0 - - + -
27J ALA* 4.1 5.2 - - - -
74J ILE* 5.9 0.7 - - + -
77J PRO* 3.0 45.8 - - + +
79J ARG* 2.7 16.4 + - - +
80J LYS 3.1 0.4 + - - -
81J THR* 1.3 82.7 - - - +
83J GLU* 1.3 58.7 + - - +
84J GLN 2.9 9.5 + - - -
85J LEU* 3.2 21.6 + - + +
86J MET* 3.2 29.7 + - + +
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Residues in contact with GLU 83 (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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79J ARG* 2.5 39.8 - - - +
80J LYS* 3.1 12.9 + - + +
82J ILE* 1.3 76.6 - - - +
84J GLN* 1.3 62.0 + - - +
85J LEU 3.3 1.2 + - - -
86J MET* 3.1 37.6 + - + +
88J LEU* 4.7 2.1 - - - +
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Residues in contact with GLN 84 (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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26J ALA* 2.7 34.7 - - - +
27J ALA* 2.7 35.7 + - + -
29J ARG* 3.4 25.2 - - - +
30J SER* 2.6 31.5 + - - -
80J LYS* 3.4 11.2 - - + +
81J THR* 3.1 7.3 - - - +
82J ILE 2.9 0.4 - - - -
83J GLU* 1.3 80.0 - - - +
85J LEU* 1.3 58.7 + - - +
86J MET 3.7 0.4 - - - -
88J LEU* 3.8 14.1 - - - +
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Residues in contact with LEU 85 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4J ILE* 5.9 1.8 - - + -
22J LYS 5.6 0.2 - - - +
23J ILE* 4.4 30.4 - - + +
24J VAL 3.8 19.7 - - - +
26J ALA* 3.4 31.2 - - + -
27J ALA* 3.4 25.1 - - + +
74J ILE* 4.5 17.0 - - + -
82J ILE* 3.2 11.3 + - + +
84J GLN* 1.3 73.7 - - - +
86J MET* 1.3 67.9 + - - +
88J LEU* 3.5 15.2 - - + +
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Residues in contact with MET 86 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82J ILE* 3.2 25.2 + - + +
83J GLU* 3.1 53.2 - - + +
84J GLN 3.7 0.2 - - - -
85J LEU* 1.3 89.0 - - - +
87J THR* 1.3 68.7 + - + +
88J LEU* 2.8 30.3 + - + +
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Residues in contact with THR 87 (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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86J MET* 1.3 85.0 - - + +
88J LEU* 1.3 58.2 + - - +
89J ASP* 4.1 8.7 + - - +
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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