Contacts of the strand formed by residues 52 - 61 (chain A) in PDB entry 1KIX
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 GLN 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A VAL* 3.9 16.2 - - + +
44A ALA* 3.4 17.0 - - + +
45A SER* 2.7 56.1 + - - +
47A THR* 4.3 9.4 + - - +
50A GLN* 3.5 15.5 + - + +
51A PRO* 1.3 74.1 - - - +
53A HIS* 1.3 66.0 + - - +
54A PHE* 5.2 1.8 - - + -
124A ARG 3.2 4.5 + - - -
125A ALA* 2.7 46.4 + - + +
127A LEU* 4.2 11.7 - - - +
136A PHE* 5.2 4.7 - - + -
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Residues in contact with HIS 53 (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 TYR* 3.4 35.9 - + - -
37A GLU* 3.4 22.2 + - + +
38A TYR* 3.3 21.7 - - + -
39A VAL* 2.9 28.2 + - - +
51A PRO* 4.0 16.2 + - + +
52A GLN* 1.3 78.2 + - - +
54A PHE* 1.3 66.7 + - - +
122A VAL 3.3 9.6 - - - +
123A HIS* 3.4 5.2 - - + -
124A ARG* 2.7 46.7 + - + -
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Residues in contact with PHE 54 (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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38A TYR* 3.6 7.1 - - - -
39A VAL* 3.2 23.3 - - + +
41A LEU* 4.0 9.4 - - + +
52A GLN* 5.0 1.8 - - + -
53A HIS* 1.3 81.4 - - - +
55A TYR* 1.3 68.7 + - - +
56A ALA* 3.8 19.7 - - + -
78A ILE* 3.8 29.2 - - + -
100A LEU* 4.2 6.5 - - + -
120A ILE* 4.8 3.1 - - + -
121A ARG* 3.4 4.7 - - - +
122A VAL* 2.9 60.3 + - + +
125A ALA* 3.9 17.0 - - + -
136A PHE* 3.7 40.6 - + + -
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Residues in contact with TYR 55 (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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38A TYR* 4.0 18.4 - + - +
39A VAL 4.9 0.6 + - - -
40A GLU* 5.8 1.0 - - - -
41A LEU* 5.2 0.5 - - - +
54A PHE* 1.3 78.3 - - - +
56A ALA* 1.3 64.3 + - - +
80A ASP* 4.5 11.6 - - - +
119A ILE* 3.8 19.3 - - + -
120A ILE 3.4 3.6 - - - -
121A ARG* 3.3 32.6 - - + -
149A PHE* 3.8 24.3 - + - -
181A ILE* 3.6 15.4 - - - +
185A GLU* 2.5 35.5 + - + -
188A ILE* 4.0 25.4 - - + -
189A LEU* 3.9 28.5 - - + -
192A LEU* 3.7 16.1 - - + +
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Residues in contact with ALA 56 (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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41A LEU* 4.0 10.1 - - + -
54A PHE* 3.8 22.0 - - + -
55A TYR* 1.3 76.1 - - - +
57A VAL* 1.3 63.3 + - - +
78A ILE* 4.0 19.5 - - + -
79A VAL 3.8 10.1 - - - +
80A ASP* 4.7 0.9 - - + -
119A ILE* 3.3 4.7 - - - +
120A ILE* 2.8 37.6 + - + +
192A LEU* 3.7 7.5 - - - +
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Residues in contact with VAL 57 (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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56A ALA* 1.3 74.8 - - - +
58A VAL* 1.3 72.1 + - - +
78A ILE* 3.2 4.8 - - - -
79A VAL* 2.9 47.8 + - + +
117A GLY 3.9 12.3 - - - +
118A ASP 3.6 9.4 - - - +
119A ILE* 4.2 3.6 - - + -
192A LEU* 3.9 21.3 - - + -
195A TRP* 3.7 26.0 - - + -
196A ALA* 4.0 11.7 - - + -
200A PHE* 3.9 22.0 - - + -
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Residues in contact with VAL 58 (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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57A VAL* 1.3 72.7 - - - +
59A ILE* 1.3 65.3 + - - +
60A ASP* 3.4 26.2 - - - +
76A LEU* 4.0 19.1 - - + -
77A LYS 3.6 5.8 - - - +
78A ILE* 4.2 2.5 - - + -
113A ILE* 4.1 29.2 - - + -
115A ARG 5.1 2.7 - - - +
116A ALA* 3.7 1.9 - - - -
117A GLY* 2.9 27.4 + - - -
118A ASP* 3.0 16.6 + - + +
119A ILE 4.9 0.2 - - - -
120A ILE* 3.7 34.5 - - + +
148A LEU* 5.4 0.9 - - + -
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Residues in contact with ILE 59 (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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57A VAL 4.1 1.1 - - - +
58A VAL* 1.3 79.8 - - - +
60A ASP* 1.3 64.1 + - + +
77A LYS* 2.8 31.9 + - + +
78A ILE 4.5 0.2 - - - +
79A VAL* 3.7 36.8 - - + -
85A LEU* 4.0 27.1 - - + -
97A TYR* 4.5 4.0 - - + -
116A ALA* 4.1 17.9 - - - +
200A PHE* 4.2 7.0 - - + -
205A VAL* 4.0 18.8 - - + -
206A ILE* 3.5 30.6 - - + +
210A MET* 4.3 12.8 - - + -
272A ARG* 4.3 3.3 + - - -
297A ILE* 5.1 1.0 - - - +
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Residues in contact with ASP 60 (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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58A VAL* 3.4 6.5 - - - +
59A ILE* 1.3 83.7 - - + +
61A ALA* 1.3 73.6 + - - +
76A LEU* 3.2 5.4 - - - +
77A LYS* 2.6 68.4 + - + +
206A ILE* 5.6 0.7 - - + -
210A MET* 6.2 0.7 - - - -
272A ARG* 2.7 33.3 + - - +
274A ARG* 2.7 24.0 + - - +
297A ILE* 3.3 12.9 - - - +
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Residues in contact with ALA 61 (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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58A VAL* 4.3 2.5 - - + -
60A ASP* 1.3 85.7 + - - +
62A THR* 1.3 67.0 + - - +
74A CYS* 4.7 1.8 - - - -
75A SER 3.3 7.2 - - - -
76A LEU* 3.9 17.5 - - + -
113A ILE* 4.0 30.1 - - + -
274A ARG* 4.2 2.9 - - - +
295A ASN* 2.8 28.4 + - - +
297A ILE* 3.5 9.1 - - + +
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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