Contacts of the helix formed by residues 97 - 109 (chain A) in PDB entry 2K0F
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A TYR 3.9 0.4 + - - -
96A ILE* 1.3 83.2 - - - +
98A ALA* 1.3 62.0 + - - +
99A ALA* 3.4 8.8 + - - +
100A GLU* 3.1 37.3 + - - +
101A LEU* 3.5 9.2 + - - +
121A ILE* 3.4 13.7 - - - +
130A GLY 4.7 0.7 - - - -
131A GLN* 4.2 18.3 + - - -
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Residues in contact with ALA 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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97A SER* 1.3 75.2 - - - +
99A ALA* 1.3 60.3 + - - +
101A LEU* 3.6 7.6 - - - +
102A ARG* 3.1 48.0 + - - +
117A VAL* 4.1 9.4 - - + +
121A ILE* 3.5 20.7 - - + +
130A GLY 4.9 0.8 + - - +
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Residues in contact with ALA 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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97A SER* 3.3 9.1 - - - +
98A ALA* 1.3 79.1 - - - +
100A GLU* 1.3 54.7 + - + +
102A ARG* 3.0 12.7 + - - +
103A HIS* 2.8 52.8 + - + +
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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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88A PHE* 3.3 16.8 - - - +
89A ASP* 3.1 4.4 - - - +
90A LYS* 2.9 36.4 + - + +
91A ASP* 3.1 11.8 + - - +
95A TYR 3.1 10.4 - - - +
96A ILE* 3.4 10.2 - - + -
97A SER* 3.1 23.0 + - - +
99A ALA* 1.3 73.8 - - + +
101A LEU* 1.3 60.2 + - - +
103A HIS* 3.2 13.3 + - + +
104A VAL* 3.0 28.6 + - - +
153A CA 2.5 31.1 - - - -
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Residues in contact with LEU 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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88A PHE* 4.2 9.6 - - + -
96A ILE* 4.4 6.0 - - + +
97A SER 3.5 15.4 + - - +
98A ALA 3.6 6.5 - - - +
100A GLU* 1.3 75.6 - - - +
102A ARG* 1.3 64.1 + - + +
104A VAL* 3.4 0.9 + - - +
105A MET* 3.0 52.0 + - + +
112A LEU* 5.7 1.6 - - + -
117A VAL* 4.1 23.3 - - + +
120A MET* 4.3 9.6 - - + -
121A ILE* 4.0 24.5 - - + +
4B TRP* 3.7 44.0 - - + -
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Residues in contact with ARG 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 ALA* 3.1 34.1 + - - +
99A ALA* 3.0 14.4 + - - +
101A LEU* 1.3 78.2 - - - +
103A HIS* 1.3 59.5 + - + +
105A MET* 3.7 4.3 - - - +
106A THR* 2.9 35.4 + - - +
112A LEU* 5.4 3.5 - - + +
114A ASP* 2.5 42.9 + - - +
117A VAL* 3.7 34.4 - - + +
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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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90A LYS* 5.0 18.8 - - + -
99A ALA* 2.8 41.2 + - + +
100A GLU* 3.4 16.2 - - + +
102A ARG* 1.3 71.2 - - + +
104A VAL* 1.3 63.6 + - + +
106A THR* 3.3 7.8 + - - -
107A ASN* 3.1 33.6 + - - +
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Residues in contact with VAL 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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35A LEU* 4.4 8.3 - - + -
87A VAL* 3.6 41.5 - - + +
88A PHE* 3.9 35.2 - - + +
90A LYS* 4.9 7.6 - - + +
100A GLU 3.0 16.6 + - - +
101A LEU 4.1 0.2 - - - +
103A HIS* 1.3 68.3 - - - +
105A MET* 1.3 59.3 + - - +
107A ASN* 3.1 10.9 + - - +
108A LEU* 2.9 46.4 + - + +
7B THR* 4.6 2.0 - - + -
11B VAL* 6.0 0.9 - - + -
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Residues in contact with MET 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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14A LEU* 6.0 0.2 - - - -
88A PHE* 4.6 2.7 - - + -
101A LEU* 3.0 42.9 + - + +
102A ARG 3.9 2.5 - - - +
104A VAL* 1.3 75.2 - - + +
106A THR* 1.3 58.9 + - - +
108A LEU* 4.3 5.1 - - - +
109A GLY 3.0 6.2 + - - -
110A GLU* 2.8 48.9 + - + +
112A LEU* 3.7 29.6 - - + -
120A MET* 4.0 13.7 - - - +
3B LYS* 3.6 15.3 - - - +
4B TRP* 4.6 7.4 - - + -
7B THR* 3.4 40.4 - - + +
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Residues in contact with THR 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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102A ARG* 2.9 23.1 + - - +
103A HIS* 3.3 11.0 + - - -
105A MET* 1.3 68.7 - - - +
107A ASN* 1.3 68.2 + - - +
109A GLY* 3.2 16.6 + - - -
110A GLU 4.1 8.8 + - - -
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Residues in contact with ASN 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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17A LYS* 5.3 2.3 + - - -
31A VAL* 4.7 3.5 - - - +
34A SER* 2.9 53.1 + - - +
35A LEU* 4.0 27.0 + - + +
90A LYS* 5.1 5.7 + - - +
103A HIS* 3.1 26.4 + - - +
104A VAL* 3.1 10.9 + - - +
106A THR* 1.3 78.9 - - - +
108A LEU* 1.3 65.9 - - - +
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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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14A LEU* 3.6 49.8 - - + +
15A PHE* 6.0 1.8 - - + -
17A LYS* 3.9 17.9 + - - -
31A VAL* 4.0 29.0 - - + +
35A LEU* 4.8 10.3 - - + -
87A VAL* 6.2 0.2 - - + -
104A VAL* 2.9 31.5 + - + +
105A MET* 4.3 5.6 - - - +
107A ASN* 1.3 78.6 - - - +
109A GLY* 1.3 58.9 + - - +
110A GLU* 5.3 0.7 - - + +
7B THR* 3.6 32.5 - - + +
10B ALA* 5.2 7.4 - - + -
11B VAL* 5.7 5.4 - - + -
14B ILE* 5.1 9.0 - - + -
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Residues in contact with GLY 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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14A LEU* 4.9 4.0 - - - -
17A LYS* 5.5 2.0 - - - -
105A MET 3.0 2.6 + - - -
106A THR 3.2 12.5 + - - -
108A LEU* 1.3 78.6 - - - +
110A GLU* 1.3 66.7 + - - +
111A LYS* 3.9 1.4 + - - +
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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