Contacts of the strand formed by residues 54 - 57 (chain J) in PDB entry 1KD1
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 VAL 54 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7J ARG* 3.5 15.0 - - + +
8J ASN* 5.8 1.8 - - - +
9J SER* 4.1 7.9 + - - +
50J VAL* 4.4 3.4 - - + -
52J LYS* 3.4 24.9 - - + +
53J PRO* 1.3 85.4 - - - +
55J GLN* 1.3 68.2 + - - +
56J ILE* 4.0 16.6 - - + -
123J ALA 3.7 0.2 - - - +
124J ARG* 3.5 3.8 - - - -
125J VAL* 2.9 31.1 + - + +
154J THR* 4.5 19.1 - - + -
155J PRO* 4.0 27.1 - - + -
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Residues in contact with GLN 55 (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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6J TYR* 2.8 31.3 - - - +
7J ARG* 3.1 19.9 + - - +
8J ASN 3.0 27.5 + - - +
9J SER* 3.7 7.6 - - - +
11J LYS* 6.1 1.5 - - - +
54J VAL* 1.3 76.1 - - - +
56J ILE* 1.3 63.9 + - - +
57J ARG* 4.1 3.2 + - - +
91J HIS* 3.2 21.7 + - - +
93J ILE* 4.5 9.2 - - - +
122J ALA* 4.3 11.4 - - + -
123J ALA 3.4 4.5 - - - +
124J ARG* 2.7 46.6 - - + +
154J THR* 4.4 5.5 + - - -
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Residues in contact with ILE 56 (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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50J VAL* 4.6 6.7 - - + -
54J VAL* 4.0 19.3 - - + -
55J GLN* 1.3 79.8 - - - +
57J ARG* 1.3 61.0 + - - +
60J ALA* 3.8 16.2 - - + -
61J LEU* 2.9 45.8 - - + +
122J ALA* 3.7 2.5 - - - -
123J ALA* 2.8 39.6 + - + +
125J VAL* 4.2 14.1 - - + -
131J ILE* 4.1 21.1 - - + -
153J VAL* 4.1 20.9 - - + -
154J THR* 5.4 3.4 - - - +
155J PRO* 4.6 6.5 - - + -
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Residues in contact with ARG 57 (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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2520A G 3.1 31.4 + - - +
1J LYS* 2.6 32.6 + - - +
2J PRO 3.7 4.8 + - - -
3J GLY* 3.1 26.5 + - - -
6J TYR* 3.8 25.1 - - + +
55J GLN 4.2 2.7 + - - +
56J ILE* 1.3 72.3 - - - +
58J HIS* 1.3 55.3 + - - +
59J ASN* 2.6 46.3 + - + +
60J ALA* 2.7 19.5 + - - +
61J LEU* 3.0 9.7 + - - +
93J ILE* 3.6 28.3 - - + -
121J THR 3.4 9.2 - - - +
122J ALA* 3.8 3.6 - - + +
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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