Contacts of the helix formed by residues 102 - 118 (chain A) in PDB entry 2KSP
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PHE* 3.7 7.9 - - - -
65A GLY 4.0 8.3 - - - +
66A LYS* 2.8 45.3 + - + +
96A ASP* 3.4 4.9 - - - +
101A LEU* 1.3 74.4 - - - +
103A ASP* 1.3 65.1 + - - +
104A GLU* 2.9 42.9 + - - +
105A GLU* 3.2 13.6 + - - +
106A PHE* 2.8 27.5 + - - +
135A LYS* 3.7 5.9 + - - -
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Residues in contact with ASP 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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50A LYS* 2.7 33.8 + - - +
53A TYR* 5.2 1.9 - - - +
54A ASP* 4.1 15.3 - - - +
57A PHE* 3.8 34.3 - - + -
58A TYR* 6.0 0.2 - - + -
65A GLY 5.0 3.1 - - - +
102A ASP* 1.3 83.8 - - - +
104A GLU* 1.3 60.6 + - - +
106A PHE* 4.2 2.1 - - - +
107A ALA* 3.1 28.1 + - - +
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Residues in contact with GLU 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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44A TRP* 3.5 22.5 - - + -
50A LYS* 3.6 12.8 - - - +
102A ASP* 2.9 24.0 + - - +
103A ASP* 1.3 79.6 - - - +
105A GLU* 1.3 66.2 + - - +
107A ALA* 3.4 2.4 + - - +
108A LEU* 3.0 27.6 + - - +
132A PRO* 3.0 27.1 - - + +
133A PRO* 5.5 1.9 - - - +
134A SER* 3.2 18.2 + - - -
135A LYS* 2.6 28.1 + - - +
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Residues in contact with GLU 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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66A LYS* 3.1 11.3 + - - -
93A ALA* 3.9 17.4 - - - +
94A ASP* 2.7 8.4 - - - +
95A VAL* 3.1 8.1 + - + +
96A ASP* 2.9 37.3 + - - +
100A LEU 2.6 8.8 - - - +
101A LEU* 3.4 14.5 - - + -
102A ASP* 3.2 14.9 + - - +
104A GLU* 1.3 78.3 - - + +
106A PHE* 1.3 58.0 + - - +
108A LEU* 3.1 8.4 + - - +
109A ALA* 2.8 26.9 + - - +
132A PRO* 6.0 0.7 - - + -
135A LYS* 4.0 10.3 - - - +
141A CA 1.8 32.9 - - - -
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Residues in contact with PHE 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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53A TYR 3.2 26.9 - - - -
56A ILE* 3.6 20.2 - - + -
57A PHE* 3.4 28.9 - + + -
60A LEU* 3.8 24.2 - - + -
67A ILE* 3.6 14.8 - - + -
72A ALA* 4.6 6.3 - - + -
75A GLU* 4.4 7.0 - - + -
76A MET* 5.6 1.8 - - - -
101A LEU* 4.0 21.0 - - + +
102A ASP 2.8 21.8 + - - +
103A ASP 4.2 1.8 - - - +
105A GLU* 1.3 71.2 - - - +
107A ALA* 1.3 61.2 + - - +
109A ALA* 3.1 8.5 + - + +
110A ASN* 2.9 62.8 + - - +
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Residues in contact with ALA 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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46A VAL* 3.6 8.5 - - + +
50A LYS* 3.4 25.1 - - + -
53A TYR* 3.4 35.3 - - + -
103A ASP 3.1 22.4 + - - +
104A GLU 3.7 1.6 - - - +
105A GLU 3.3 0.2 - - - -
106A PHE* 1.3 77.3 - - - +
108A LEU* 1.3 58.5 + - - +
111A HIS* 2.8 29.3 + - - +
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Residues in contact with LEU 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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44A TRP* 3.7 4.5 - - + -
46A VAL* 3.4 28.0 - - + -
93A ALA* 4.1 13.7 - - + +
95A VAL* 4.6 10.5 - - + -
104A GLU 3.0 13.1 + - - +
105A GLU* 3.4 8.5 - - - +
107A ALA* 1.3 74.1 - - - +
109A ALA* 1.3 59.1 + - - +
111A HIS* 3.2 7.0 + - + +
112A LEU* 2.8 44.8 + - + +
126A LEU* 5.7 5.8 - - + -
130A LEU* 3.4 38.4 - - + +
132A PRO* 3.4 28.9 - - + -
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Residues in contact with ALA 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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76A MET* 3.6 25.8 - - + -
89A ILE* 3.4 8.2 - - + +
90A TRP* 5.8 0.2 - - - -
93A ALA* 3.5 17.8 - - + +
101A LEU* 4.1 9.9 - - + -
105A GLU 2.8 13.4 + - - +
106A PHE* 3.2 14.8 - - + +
108A LEU* 1.3 77.5 - - - +
110A ASN* 1.3 58.4 + - - +
112A LEU 3.3 0.2 + - - -
113A ILE* 3.0 34.8 + - - +
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Residues in contact with ASN 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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53A TYR* 3.4 39.1 + - + +
56A ILE* 4.4 6.3 - - - +
75A GLU* 4.8 9.1 - - - +
76A MET* 5.2 2.0 - - - -
79A SER* 5.7 0.6 + - - -
106A PHE* 2.9 59.1 + - - +
109A ALA* 1.3 74.7 - - - +
111A HIS* 1.3 61.0 + - - +
113A ILE* 3.3 17.7 + - - +
114A LYS* 2.8 30.5 + - - +
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Residues in contact with HIS 111 (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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45A VAL* 3.8 24.7 - - + +
46A VAL* 4.3 15.9 - - + -
49A ASP* 2.7 36.8 + - - +
53A TYR* 3.9 8.4 - - + -
107A ALA 2.8 19.6 + - - +
108A LEU* 3.5 10.3 - - + +
110A ASN* 1.3 76.3 - - - +
112A LEU* 1.3 66.5 + - + +
114A LYS* 3.2 7.7 + - + +
115A VAL* 3.0 45.3 + - + +
130A LEU* 4.7 9.4 - - + +
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Residues in contact with LEU 112 (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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89A ILE* 3.6 36.6 - - + +
92A LEU* 4.0 11.4 - - + -
93A ALA* 4.1 9.6 - - + +
108A LEU* 2.8 29.9 + - + +
109A ALA 3.7 3.1 - - - +
111A HIS* 1.3 82.3 - - + +
113A ILE* 1.3 66.2 + - - +
115A VAL* 3.1 11.8 + - + +
116A LYS* 3.1 24.4 + - - +
122A LEU* 3.7 38.0 - - + +
126A LEU* 5.3 6.5 - - + -
130A LEU* 5.2 13.7 - - + -
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Residues in contact with ILE 113 (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 GLU 6.0 0.2 - - - -
76A MET* 3.7 36.3 - - + -
79A SER* 3.9 22.0 - - - +
81A LEU* 3.8 30.1 - - + -
86A LEU* 6.3 1.8 - - + -
89A ILE* 3.8 19.5 - - + +
109A ALA 3.0 21.2 + - - +
110A ASN* 3.3 17.7 + - - +
112A LEU* 1.3 74.9 - - - +
114A LYS* 1.3 58.2 + - - +
116A LYS* 3.1 10.6 + - - +
117A LEU* 2.9 34.8 + - + +
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Residues in contact with LYS 114 (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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49A ASP* 4.9 5.2 - - - +
53A TYR* 3.8 17.9 - - - +
110A ASN 2.8 13.9 + - - +
111A HIS* 3.4 11.9 - - + +
112A LEU 3.2 0.2 - - - -
113A ILE* 1.3 75.0 - - - +
115A VAL* 1.3 56.1 + - + +
117A LEU* 2.9 15.4 + - + +
118A GLU* 2.7 74.2 + - + +
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Residues in contact with VAL 115 (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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111A HIS* 3.0 38.9 + - + +
112A LEU* 3.1 16.4 + - + +
114A LYS* 1.3 75.7 - - + +
116A LYS* 1.3 62.4 + - - +
118A GLU* 3.2 14.7 + - - +
120A HIS* 3.0 40.6 + - + +
121A GLU 4.3 17.3 - - - +
122A LEU* 4.7 5.2 - - + +
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Residues in contact with LYS 116 (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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81A LEU* 4.6 17.0 - - + -
85A VAL* 3.9 37.6 - - + +
89A ILE* 4.2 2.5 - - + -
112A LEU 3.1 16.8 + - - +
113A ILE* 3.3 9.9 - - - +
115A VAL* 1.3 76.8 - - - +
117A LEU* 1.3 56.8 + - - +
119A GLY* 3.0 21.0 + - - -
120A HIS 3.0 20.0 + - - +
121A GLU* 3.8 26.6 + - + +
122A LEU* 3.9 13.2 - - + -
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Residues in contact with LEU 117 (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 SER* 4.4 9.0 - - - +
81A LEU* 3.7 30.5 - - + -
113A ILE* 2.9 30.3 + - + +
114A LYS* 2.9 15.7 + - + +
116A LYS* 1.3 71.4 - - - +
118A GLU* 1.3 64.0 + - - +
119A GLY* 3.0 9.8 + - - -
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Residues in contact with GLU 118 (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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114A LYS* 2.7 63.0 + - + +
115A VAL* 3.4 12.1 - - - +
116A LYS 3.2 0.4 - - - -
117A LEU* 1.3 79.7 - - - +
119A GLY* 1.3 58.7 + - - +
120A HIS* 3.4 27.9 + - + +
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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