Contacts of the helix formed by residues 96 - 110 (chain A) in PDB entry 1KPH
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 SER 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 5.4 0.9 - - - -
13A GLN* 4.3 2.2 - - - +
16A TYR* 3.6 19.5 + - - +
17A ASP* 2.7 26.2 + - - -
94A THR* 3.2 3.0 + - - +
95A LEU* 1.3 76.6 - - - +
97A LYS* 1.3 57.7 + - - +
99A GLN* 3.1 43.1 + - - +
100A ALA* 2.9 30.3 + - - +
120A LEU* 3.5 2.7 - - - +
1900A SAH 3.8 3.4 + - - -
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Residues in contact with LYS 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 PHE* 5.5 1.0 - - - -
13A GLN* 2.9 35.7 + - - +
17A ASP* 3.0 16.5 + - - +
95A LEU 3.6 1.0 + - - -
96A SER* 1.3 70.8 - - - +
98A ASN* 1.3 62.8 + - - +
100A ALA* 3.2 3.0 + - - +
101A ASN* 3.0 41.0 + - - +
120A LEU* 3.9 26.2 - - + +
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Residues in contact with ASN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR 4.2 2.2 + - - +
17A ASP* 2.7 53.9 + - - +
19A SER* 4.2 9.5 - - - +
20A ASP* 3.3 29.5 + - - +
96A SER* 4.2 1.8 - - - +
97A LYS* 1.3 77.0 - - - +
99A GLN* 1.3 55.5 + - - +
101A ASN* 3.6 8.5 + - - +
102A HIS* 3.0 28.4 + - - +
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Residues in contact with GLN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.7 15.7 - - - -
74A GLY* 3.4 25.4 - - - +
75A TRP* 3.4 59.5 - - + +
94A THR* 2.7 20.0 + - + +
96A SER* 3.1 23.7 + - - +
97A LYS 3.2 0.6 - - - -
98A ASN* 1.3 73.8 - - - +
100A ALA* 1.3 66.0 + - - +
102A HIS* 3.7 0.3 - - - +
103A VAL* 2.9 32.1 + - - +
1900A SAH 2.5 26.0 + - - +
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Residues in contact with ALA 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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94A THR* 3.9 13.4 - - + +
96A SER 2.9 17.5 + - - +
97A LYS* 3.5 5.2 - - - +
99A GLN* 1.3 77.0 - - - +
101A ASN* 1.3 60.9 + - - +
103A VAL 3.9 0.2 - - - -
104A GLN* 3.0 29.8 + - - +
118A VAL* 3.9 15.8 - - + +
120A LEU* 4.0 30.1 - - + +
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Residues in contact with ASN 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 LYS* 3.0 22.6 + - - +
98A ASN* 3.9 8.2 - - - +
100A ALA* 1.3 79.7 - - - +
102A HIS* 1.3 65.6 + - - +
104A GLN* 3.2 9.5 + - - +
105A GLN* 3.2 25.6 + - - +
120A LEU* 6.3 0.4 - - - +
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Residues in contact with HIS 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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20A ASP* 4.0 10.6 + - - +
24A ARG* 4.1 24.1 + - - -
31A GLN* 4.9 6.5 - - + +
75A TRP* 3.6 48.8 + + + +
98A ASN 3.0 19.4 + - - +
99A GLN 3.7 3.8 - - - +
101A ASN* 1.3 76.3 - - - +
103A VAL* 1.3 62.2 + - - +
105A GLN* 3.1 18.8 + - - +
106A LEU* 3.2 29.8 + - + +
249D GLN* 5.6 7.6 - - + -
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Residues in contact with VAL 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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73A CYS* 4.5 2.2 - - - -
74A GLY 3.6 7.6 - - - +
75A TRP* 3.4 34.1 - - - +
76A GLY* 3.6 6.7 - - - +
79A MET* 4.1 20.9 - - + -
80A MET* 5.6 2.7 - - - -
99A GLN 2.9 20.9 + - - +
102A HIS* 1.3 71.8 - - - +
104A GLN* 1.3 60.1 + - - +
106A LEU* 3.1 12.6 + - + +
107A VAL* 2.9 32.3 + - + +
118A VAL* 3.7 30.7 - - + -
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Residues in contact with GLN 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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100A ALA 3.0 20.1 + - - +
101A ASN* 3.3 11.2 - - - +
102A HIS 3.2 0.4 - - - -
103A VAL* 1.3 77.7 - - - +
105A GLN* 1.3 65.9 + - - +
107A VAL* 3.6 14.5 + - - +
108A ALA* 3.0 28.1 + - - +
118A VAL* 3.6 21.6 - - + +
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Residues in contact with GLN 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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101A ASN 3.2 10.6 + - - +
102A HIS* 3.1 12.3 + - - +
104A GLN* 1.3 86.4 + - - +
106A LEU* 1.3 61.5 + - + +
108A ALA* 3.7 10.4 - - - +
109A ASN* 2.8 55.6 + - - +
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Residues in contact with LEU 106 (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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75A TRP 3.6 24.5 - - - +
76A GLY* 4.7 2.5 - - - -
77A ALA* 6.0 0.2 - - - -
80A MET* 4.0 35.9 - - + +
102A HIS* 3.6 28.3 - - + +
103A VAL* 3.1 16.5 + - + +
105A GLN* 1.3 79.3 - - + +
107A VAL* 1.3 61.7 + - - +
109A ASN* 3.7 3.7 - - - +
110A SER* 3.0 25.5 + - - -
248D GLY* 5.2 14.4 - - - +
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Residues in contact with VAL 107 (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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79A MET* 5.2 2.7 - - + -
80A MET* 5.1 5.2 - - - -
103A VAL* 2.9 30.9 + - + +
104A GLN* 3.7 17.0 - - - +
106A LEU* 1.3 75.9 - - - +
108A ALA* 1.3 63.2 + - - +
109A ASN 3.3 0.7 + - - -
110A SER* 3.3 19.9 + - - +
116A LYS* 3.6 52.3 + - + +
117A ARG* 4.7 1.3 - - - +
118A VAL* 4.7 9.2 - - + +
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Residues in contact with ALA 108 (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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104A GLN* 3.0 25.7 + - - +
105A GLN* 3.7 19.1 - - - +
107A VAL* 1.3 78.6 - - - +
109A ASN* 1.3 63.5 + - - +
110A SER 3.8 3.1 + - - +
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Residues in contact with ASN 109 (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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105A GLN* 2.8 46.0 + - - +
106A LEU* 3.7 3.8 - - - +
108A ALA* 1.3 79.7 - - - +
110A SER* 1.3 66.4 + - - +
111A GLU* 3.6 5.9 + - - +
248D GLY* 6.1 3.7 - - - -
251D ILE* 6.5 1.3 - - - -
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Residues in contact with SER 110 (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 MET* 4.1 11.9 - - - +
84A GLU* 5.3 1.4 + - - -
106A LEU 3.0 16.2 + - - -
107A VAL 3.3 10.3 + - - +
108A ALA 4.5 2.9 - - - +
109A ASN* 1.3 80.2 - - - +
111A GLU* 1.3 62.1 + - - +
112A ASN* 3.0 15.5 + - - +
116A LYS* 3.0 35.2 + - - -
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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