Contacts of the strand formed by residues 71 - 79 (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 ARG 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LYS* 3.9 0.3 - - - -
67A THR* 3.0 39.9 + - + +
68A ASN* 3.3 14.1 + - + +
69A GLN 3.0 9.4 + - - +
70A GLU* 1.3 88.7 + - - +
72A TYR* 1.3 69.1 + - - +
73A ILE* 4.9 2.2 - - + -
103A TYR* 4.2 10.7 - - + +
104A ALA 3.7 4.2 + - - -
105A LYS* 4.2 14.8 - - - +
141A PHE* 3.1 41.1 - - - -
3D T 5.4 0.4 + - - -
4D T 3.3 25.9 + - - +
5D G 3.6 33.0 - - - -
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Residues in contact with TYR 72 (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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65A TYR* 3.3 8.1 - - - -
66A LYS* 3.3 53.2 - - + +
70A GLU* 5.0 4.0 - - - -
71A ARG* 1.3 80.5 - - - +
73A ILE* 1.3 70.5 + - - +
103A TYR* 3.6 2.3 - - - +
104A ALA 2.7 34.9 + - - +
105A LYS 3.5 14.1 - - - -
106A ARG* 3.4 29.2 - - - +
107A PHE* 3.6 31.9 - + + +
110A LEU* 3.7 17.3 - - + -
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Residues in contact with ILE 73 (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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64A PRO* 3.6 0.9 - - - +
65A TYR* 2.8 65.5 + - + +
67A THR* 3.9 13.4 - - + +
71A ARG* 4.9 1.6 - - + -
72A TYR* 1.3 82.8 - - - +
74A CYS* 1.3 73.5 + - - +
75A SER* 4.1 1.6 - - - +
101A VAL* 4.0 6.7 - - + -
102A LEU 3.4 7.0 - - - +
103A TYR* 3.8 31.9 - - + -
110A LEU* 3.5 4.7 - - - +
5D G 3.3 34.1 - - - +
6D G 3.7 15.5 - - - +
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Residues in contact with CYS 74 (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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61A ALA* 4.7 3.1 - - - -
62A THR* 3.5 27.6 - - - -
63A PHE 4.7 0.2 - - - -
64A PRO* 4.5 5.2 - - + -
73A ILE* 1.3 79.1 - - - +
75A SER* 1.3 59.8 + - - +
76A LEU* 3.3 28.6 - - + +
101A VAL* 3.7 0.2 - - - -
102A LEU* 2.9 37.8 + - + -
110A LEU* 3.9 19.7 - - + +
111A PRO* 3.9 23.6 - - + -
113A ILE* 5.2 0.7 - - - -
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Residues in contact with SER 75 (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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60A ASP 4.6 0.2 - - - -
61A ALA* 3.3 2.9 - - - -
62A THR* 3.0 44.4 + - - +
65A TYR* 5.1 2.5 - - - -
73A ILE* 4.1 5.0 - - - +
74A CYS* 1.3 72.7 - - - +
76A LEU* 1.3 65.0 + - - +
99A THR* 5.7 1.9 - - - -
100A LEU 3.6 5.8 + - - -
101A VAL* 4.6 5.3 - - - +
274A ARG* 4.7 4.5 + - - -
6D G 3.2 17.4 + - - -
7D G 2.6 30.5 + - - -
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Residues in contact with LEU 76 (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* 4.0 14.6 - - + -
60A ASP 3.2 8.1 - - - +
61A ALA* 3.9 9.4 - - + -
74A CYS* 3.3 30.7 - - - +
75A SER* 1.3 79.9 + - - +
77A LYS* 1.3 68.5 + - - +
78A ILE* 4.6 2.0 - - + -
99A THR* 3.2 8.8 - - - +
100A LEU* 2.7 53.4 + - + +
102A LEU* 4.1 17.0 - - + -
113A ILE* 3.2 32.3 - - + -
120A ILE* 3.9 17.9 - - + -
274A ARG* 6.1 0.4 - - - +
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Residues in contact with LYS 77 (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* 3.6 1.0 - - - -
59A ILE* 2.8 42.1 + - + -
60A ASP* 2.6 46.5 + - + +
76A LEU* 1.3 76.8 - - - +
78A ILE* 1.3 64.5 + - - +
97A TYR* 3.4 40.2 - - + -
98A ALA 3.4 4.7 - - - -
99A THR* 4.8 6.1 - - + -
210A MET* 3.6 22.7 - - + -
272A ARG* 4.6 0.8 - - - +
274A ARG* 3.6 6.0 - - - +
7D G 2.8 30.3 + - - -
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Residues in contact with ILE 78 (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* 3.8 22.1 - - + +
54A PHE* 3.8 32.1 - - + -
56A ALA* 4.0 10.8 - - + -
57A VAL 3.2 11.4 - - - +
58A VAL* 4.2 15.7 - - + -
59A ILE 4.6 0.4 - - - +
76A LEU* 4.6 10.5 - - + -
77A LYS* 1.3 79.9 - - - +
79A VAL* 1.3 67.6 + - - +
97A TYR* 3.8 0.5 - - - +
98A ALA* 2.7 49.6 + - + +
99A THR 4.3 2.5 - - - +
100A LEU* 4.0 16.6 - - + -
120A ILE* 4.5 7.2 - - + -
136A PHE* 4.1 8.1 - - + -
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Residues in contact with VAL 79 (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* 3.7 4.7 - - - -
56A ALA* 3.8 1.7 - - - +
57A VAL* 2.9 45.3 + - + +
59A ILE* 3.7 31.9 - - + -
78A ILE* 1.3 81.6 - - - +
80A ASP* 1.3 63.7 + - - +
83A LEU 3.3 14.4 - - - +
84A TYR* 4.0 13.0 - - + -
85A LEU* 4.5 4.5 - - + +
97A TYR* 3.6 22.2 - - + -
195A TRP* 4.1 3.4 - - + -
199A TYR* 4.0 20.9 - - + +
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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