Contacts of the helix formed by residues 90 - 101 (chain A) in PDB entry 2KJD
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 ASP 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A MET 5.5 0.5 - - - +
9A ARG 4.2 4.9 - - - +
11A ARG* 2.8 42.2 + - - -
52A ARG* 4.8 6.4 - - - +
54A GLN 5.4 0.4 - - - -
55A ASP* 3.7 14.9 - - - +
89A VAL* 1.3 77.0 - - - +
91A ARG* 1.3 57.3 + - - +
92A GLU* 3.3 6.1 - - + +
93A THR* 2.8 29.6 + - - +
94A ASP* 2.7 31.4 + - - +
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 5.1 11.3 + - + +
55A ASP* 4.7 1.8 + - - -
90A ASP* 1.3 73.3 - - - +
92A GLU* 1.3 91.1 + - - +
94A ASP* 3.2 4.0 + - - +
95A GLU* 2.8 54.9 + - + +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.0 21.8 - - + +
90A ASP* 3.3 5.3 - - + +
91A ARG* 1.3 121.2 + - - +
93A THR* 1.3 63.0 + - - +
95A GLU* 3.6 6.6 + - - +
96A PHE* 3.1 22.7 + - - +
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Residues in contact with THR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A MET 4.6 1.2 + - - -
8A LEU* 3.3 41.1 - - - +
9A ARG 3.7 12.8 + - - +
10A PRO 4.0 1.3 - - - -
89A VAL* 4.0 8.1 - - + -
90A ASP* 2.8 35.6 + - - +
91A ARG 3.2 0.2 - - - -
92A GLU* 1.3 79.1 - - - +
94A ASP* 1.3 56.4 + - - +
96A PHE* 3.2 8.5 + - - +
97A PHE* 2.9 49.1 + - + -
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 5.8 2.3 - - - -
56A ARG* 2.6 37.6 + - - -
89A VAL* 3.7 15.3 - - + +
90A ASP 2.7 21.4 + - - +
91A ARG* 3.8 4.7 - - - +
93A THR* 1.3 71.0 - - - +
95A GLU* 1.3 56.1 + - - +
97A PHE* 3.2 9.8 + - - +
98A LYS* 2.6 67.7 + - - +
104A PRO* 5.3 0.3 - - - +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ARG* 2.8 48.9 + - + +
92A GLU* 3.9 7.4 - - - +
94A ASP* 1.3 75.8 - - - +
96A PHE* 1.3 61.0 + - - +
98A LYS* 2.6 42.2 + - - +
99A LYS* 3.1 26.8 + - - +
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Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 5.2 5.8 - - + -
8A LEU* 3.6 39.3 - - + -
92A GLU 3.1 15.2 + - - +
93A THR* 3.2 10.1 - - - +
95A GLU* 1.3 77.6 - - - +
97A PHE* 1.3 70.6 + + - +
99A LYS* 3.1 51.0 - - - +
100A CYS* 3.3 16.1 + - + +
113A LEU* 3.8 27.1 - - + -
114A PRO* 3.8 36.1 - - + -
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Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU 4.2 2.5 - - - -
10A PRO* 3.9 16.2 - - + -
89A VAL* 4.2 2.2 - - + -
93A THR* 2.9 48.1 + - + -
94A ASP* 3.2 11.4 + - - +
96A PHE* 1.3 78.3 - + - +
98A LYS* 1.3 66.6 + - - +
100A CYS* 3.3 0.9 + - - -
101A ARG* 3.0 4.0 + - - -
102A VAL* 2.9 74.5 + - + +
104A PRO* 3.6 36.8 - - + -
108A HIS* 3.9 19.3 - + + -
113A LEU* 4.4 9.4 - - + -
114A PRO* 4.4 9.2 - - + -
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 6.1 4.2 - - - +
94A ASP* 2.6 51.1 + - - +
95A GLU* 2.6 35.6 + - - +
96A PHE 3.3 0.2 - - - -
97A PHE* 1.3 73.1 - - - +
99A LYS* 1.3 63.1 + - - +
101A ARG* 3.1 22.4 + - - +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLU 3.1 12.1 + - - +
96A PHE* 3.1 47.8 - - - +
98A LYS* 1.3 79.2 - - - +
100A CYS* 1.3 63.7 + - + +
101A ARG* 3.4 24.3 + - - +
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Residues in contact with CYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PHE* 3.3 20.2 + - + +
97A PHE* 4.1 0.9 - - - +
98A LYS 3.1 0.4 - - - -
99A LYS* 1.3 88.1 - - + +
101A ARG* 1.3 74.6 + - - +
102A VAL* 3.4 24.7 - - + +
114A PRO* 4.1 13.0 - - + -
115A VAL 3.9 22.0 - - - -
116A PRO* 5.3 0.9 - - - -
117A PHE* 4.9 4.7 - - - -
118A THR* 3.6 26.5 + - - +
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE 3.0 6.0 + - - -
98A LYS 3.1 19.1 + - - +
99A LYS* 3.4 17.8 + - - +
100A CYS* 1.3 82.9 + - - +
102A VAL* 1.3 59.7 + - - +
103A ILE* 4.3 3.5 + - - +
117A PHE* 5.6 3.6 + - - +
118A THR* 4.6 11.7 + - - -
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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