Contacts of the helix formed by residues 96 - 105 (chain A) in PDB entry 1KI1
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 LYS 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASP* 4.7 2.1 + - - +
62A GLU* 2.9 26.0 + - - +
63A ASP* 4.6 6.7 + - - +
68A ARG* 3.5 32.7 - - - +
92A ASN* 2.7 36.4 + - - +
94A LYS 3.5 0.2 - - - -
95A GLU* 1.3 77.0 - - + +
97A TRP* 1.3 94.7 + - + +
99A PRO* 3.4 5.5 - - - +
100A GLU* 3.2 25.2 + - - +
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Residues in contact with TRP 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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9A VAL* 4.1 14.8 - - + -
10A GLY* 3.4 43.7 - - - -
11A ASP* 2.7 33.4 + - - +
58A THR* 6.0 1.8 - - - -
62A GLU* 4.2 11.7 - - + -
68A ARG* 3.2 39.9 - - - -
72A TYR* 4.2 6.7 - - - -
80A VAL* 3.9 19.7 - - + -
89A SER 5.1 0.9 - - - -
92A ASN* 3.0 23.8 + - + +
93A VAL* 3.9 9.9 - - + +
96A LYS* 1.3 99.6 - - + +
98A VAL* 1.3 65.9 + - - +
100A GLU* 3.3 9.2 + - - +
101A ILE* 3.2 30.4 + - + +
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Residues in contact with VAL 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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80A VAL* 4.6 6.1 - - + -
93A VAL* 2.9 33.3 + - + +
97A TRP* 1.3 69.2 - - - +
99A PRO* 1.3 71.1 - - + +
101A ILE* 3.6 6.9 - - + +
102A THR* 2.8 41.7 + - - +
110A PHE* 3.9 35.0 - - + -
149A LEU* 3.7 38.1 - - + +
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Residues in contact with PRO 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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93A VAL 3.8 0.7 - - - +
94A LYS 3.1 28.5 - - - +
95A GLU* 3.8 12.1 - - - +
96A LYS 3.4 14.1 - - - +
98A VAL* 1.3 93.0 - - + +
100A GLU* 1.3 59.7 + - - +
102A THR* 3.8 4.6 - - - -
103A HIS* 3.1 24.6 + - - +
149A LEU* 6.0 0.4 - - + -
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Residues in contact with GLU 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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65A ASP* 4.9 2.9 - - - +
68A ARG* 2.5 49.6 + - - +
69A PRO* 5.2 2.9 - - - -
72A TYR* 2.7 36.1 + - + +
96A LYS* 3.2 17.0 + - + +
97A TRP* 3.7 6.1 - - - +
98A VAL 3.1 0.8 - - - -
99A PRO* 1.3 82.3 - - - +
101A ILE* 1.3 63.1 + - + +
103A HIS* 3.3 5.0 + - - +
104A HIS* 3.1 35.4 + - + +
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Residues in contact with ILE 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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9A VAL* 4.6 10.5 - - + -
72A TYR* 4.4 17.5 - - + +
78A PHE* 3.8 48.2 - - + -
80A VAL* 3.8 26.2 - - + -
97A TRP* 3.2 12.5 + - + +
98A VAL* 3.6 11.7 - - - +
100A GLU* 1.3 74.5 - - + +
102A THR* 1.3 65.7 + - - +
104A HIS* 4.5 3.4 - - - +
105A CYS* 2.8 34.8 + - - +
108A THR 5.4 2.6 - - - +
110A PHE* 3.9 22.7 - - + -
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Residues in contact with THR 102 (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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98A VAL* 2.8 35.2 + - - +
99A PRO* 3.8 5.6 - - - -
101A ILE* 1.3 78.6 - - - +
103A HIS* 1.3 65.1 + - - +
105A CYS 4.6 3.6 - - - -
106A PRO* 3.2 30.9 - - + +
110A PHE* 5.2 3.5 - - - -
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Residues in contact with HIS 103 (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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99A PRO 3.1 18.0 + - - +
100A GLU* 3.5 6.1 - - - +
102A THR* 1.3 79.7 - - - +
104A HIS* 1.3 85.5 + + - +
106A PRO* 4.0 5.5 - - - +
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Residues in contact with HIS 104 (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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66A ARG* 5.0 14.1 + - - -
69A PRO* 3.5 28.3 + - + +
72A TYR* 3.8 31.4 - + + +
100A GLU* 3.1 34.9 + - + +
101A ILE 4.5 0.2 - - - +
103A HIS* 1.3 99.4 - + - +
105A CYS* 1.3 67.7 + - - +
106A PRO* 3.6 5.1 - - - +
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Residues in contact with CYS 105 (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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72A TYR* 3.7 34.1 - - - -
73A PRO* 5.3 2.0 - - - -
74A GLN 5.6 0.7 - - - -
75A THR* 4.8 2.2 - - - -
78A PHE* 3.8 20.2 - - + -
101A ILE 2.8 24.4 + - - +
102A THR* 4.6 1.2 - - - -
104A HIS* 1.3 83.2 - - - +
106A PRO* 1.3 60.9 - - - +
107A LYS 3.3 2.5 - - - -
108A THR* 3.0 46.1 + - - +
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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