Contacts of the strand formed by residues 130 - 136 (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 HIS 130 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003A U 5.1 0.2 + - - -
47J GLU* 3.0 24.6 + - + +
48J LEU 3.2 12.3 - - - +
49J VAL* 4.2 7.6 - - + +
86J ARG* 2.7 73.5 + - - +
87J LYS* 4.5 5.6 - - - -
125J VAL* 5.8 0.2 - - - -
128J ALA 4.9 2.6 + - - -
129J ASN* 1.3 81.9 - - - +
131J ILE* 1.3 59.6 + - - +
133J ILE* 3.1 18.4 - - + -
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Residues in contact with ILE 131 (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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48J LEU* 2.9 25.5 + - + +
50J VAL* 4.4 18.2 - - + -
56J ILE* 4.1 18.6 - - + -
61J LEU* 3.5 31.6 - - + -
85J ILE* 3.3 10.4 - - + -
86J ARG* 3.0 28.4 + - - -
87J LYS* 4.3 22.9 - - + -
125J VAL* 5.0 6.7 - - + +
129J ASN 3.7 2.0 + - - -
130J HIS* 1.3 74.5 - - - +
132J PHE* 1.3 86.7 + - + +
153J VAL* 4.9 6.7 - - + -
157J ILE* 5.0 1.8 - - + -
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Residues in contact with PHE 132 (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 MET* 4.7 0.2 - - + -
48J LEU* 2.8 46.9 + - + +
61J LEU* 4.6 2.0 - - + -
64J ALA* 4.1 18.4 - - + -
65J ARG* 3.6 42.0 - - + -
83J PHE* 4.1 15.5 - + + -
84J ARG 3.3 4.5 - - - -
85J ILE* 3.3 41.3 - - + -
131J ILE* 1.3 107.0 - - + +
133J ILE* 1.3 72.0 + - - +
146J TRP* 3.8 24.0 - - + +
149J ALA* 4.4 8.7 - - + -
153J VAL* 5.9 0.7 - - + -
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Residues in contact with ILE 133 (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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45J GLN* 3.9 11.0 - - + +
46J VAL 3.5 7.4 - - - +
47J GLU* 2.9 52.3 - - + +
83J PHE* 3.6 0.6 - - - -
84J ARG* 2.7 43.1 + - + +
86J ARG* 2.6 34.5 - - - +
130J HIS* 3.1 11.4 - - + -
132J PHE* 1.3 80.7 - - - +
134J ALA* 1.3 60.5 + - - +
135J TRP* 3.3 43.3 - - + -
146J TRP* 3.9 1.6 - - - -
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Residues in contact with ALA 134 (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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45J GLN* 3.5 3.1 - - - +
46J VAL 2.9 28.0 + - - +
81J TYR* 5.9 2.9 - - + -
82J LYS 3.3 7.2 - - - +
83J PHE* 3.4 22.0 - - + -
133J ILE* 1.3 75.4 - - - +
135J TRP* 1.3 70.5 + - - +
136J VAL* 4.2 1.1 - - + -
142J VAL* 3.6 22.9 - - + -
146J TRP* 3.4 13.4 - - + -
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Residues in contact with TRP 135 (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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40J PRO* 4.1 30.7 - - + +
42J TYR* 3.6 23.8 - - + -
44J ALA 3.5 5.4 - - - -
45J GLN* 2.8 53.7 - - + +
81J TYR* 3.2 13.3 - - - +
82J LYS* 2.8 63.9 + - + -
84J ARG* 2.8 59.0 - - + -
86J ARG* 5.1 0.7 - - - -
133J ILE* 3.3 25.1 - - + -
134J ALA* 1.3 75.5 - - - +
136J VAL* 1.3 60.0 + - - +
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Residues in contact with VAL 136 (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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42J TYR* 3.7 10.9 - - - +
43J PRO* 3.7 1.9 - - - +
44J ALA* 2.9 52.9 + - + +
46J VAL* 5.0 4.9 - - + -
80J ASN 4.8 7.0 - - - +
81J TYR* 4.7 7.0 - - + -
134J ALA* 5.7 1.8 - - + +
135J TRP* 1.3 74.8 - - - +
137J ASN* 1.3 81.6 + - - +
139J ASP* 3.5 28.7 - - + +
140J PRO* 4.5 8.7 - - + -
142J VAL* 3.7 28.9 - - + -
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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