Contacts of the helix formed by residues 102 - 111 (chain A) in PDB entry 2KBX
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 VAL 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A HIS* 4.2 1.1 - - - -
93A ILE* 4.1 15.7 - - + +
96A VAL* 3.5 22.4 - - + -
100A GLY 2.9 4.3 + - - +
101A ASN* 1.3 74.9 - - - +
103A PRO* 1.3 76.1 - - + +
104A LEU* 3.1 29.6 - - + +
105A HIS* 2.8 38.1 + - + +
106A TYR* 3.4 5.4 + - - -
124A ALA* 5.4 2.2 - - + -
128A ILE* 4.2 27.6 - - + -
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Residues in contact with PRO 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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71A LEU* 4.2 29.4 - - + +
72A HIS* 4.1 17.0 - - + +
75A ALA* 4.1 6.9 - - + +
87A LEU* 5.6 0.9 - - + -
92A ASP 5.6 0.2 - - - +
93A ILE* 3.8 27.1 - - + +
95A ALA 5.6 1.8 - - - +
96A VAL* 5.4 0.9 - - + -
101A ASN 4.3 2.7 - - - +
102A VAL* 1.3 94.0 - - + +
104A LEU* 1.3 54.9 + - - +
106A TYR* 3.3 7.1 + - + +
107A ALA* 2.7 27.7 + - - +
119A LEU* 3.7 31.4 - - + -
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Residues in contact with LEU 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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102A VAL* 2.9 16.7 + - + +
103A PRO* 1.3 76.9 - - - +
105A HIS* 1.3 67.4 + - - +
107A ALA* 3.8 2.0 - - + -
108A CYS* 3.0 23.8 + - + +
116A ALA* 3.2 52.5 - - + +
119A LEU* 3.8 15.3 - - + +
120A VAL* 4.8 9.4 - - + +
124A ALA* 5.7 4.7 - - + -
125A LEU 4.8 2.9 - - - +
126A VAL* 4.0 29.6 - - + -
128A ILE* 6.1 0.7 - - + -
136A PRO* 3.9 24.4 - - + +
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Residues in contact with HIS 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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100A GLY 4.9 2.7 - - - -
101A ASN* 4.4 8.1 - - + -
102A VAL* 2.8 41.3 + - + +
104A LEU* 1.3 78.4 - - - +
106A TYR* 1.3 59.5 + - + +
108A CYS* 3.7 1.7 + - - +
109A PHE* 3.1 25.7 + - - +
128A ILE* 4.5 15.0 - - + -
130A ASN* 3.4 36.1 + - + +
134A GLU 2.8 30.8 + - - -
135A MET* 3.7 18.7 - - - +
136A PRO* 4.1 9.1 - - + +
42B PHE* 6.0 6.7 - - + -
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Residues in contact with TYR 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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68A ASP* 6.1 0.7 - - - -
72A HIS* 4.1 35.7 - + + +
75A ALA* 4.9 4.0 - - + -
76A SER* 4.9 12.1 - - - +
101A ASN* 3.5 42.0 + - + -
102A VAL 3.4 2.6 + - - +
103A PRO* 3.3 8.2 + - + +
104A LEU 3.1 0.4 - - - -
105A HIS* 1.3 80.5 - - + +
107A ALA* 1.3 66.0 + - - +
109A PHE* 2.9 26.9 + + + +
110A TRP* 3.2 29.5 + - - -
39B ALA* 2.5 41.2 + - + +
40B GLN* 4.2 7.6 + - - +
42B PHE* 3.4 15.9 - + - -
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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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75A ALA* 4.3 13.4 - - + +
103A PRO 2.7 21.2 + - - +
104A LEU* 3.4 17.3 - - + +
106A TYR* 1.3 74.8 - - - +
108A CYS* 1.3 57.0 + - - +
110A TRP* 3.7 0.7 + - - +
111A GLY 3.2 8.1 + - - -
112A GLN* 3.1 30.9 + - - +
115A VAL* 3.9 23.6 - - + -
116A ALA* 4.5 3.1 - - + -
119A LEU* 4.1 8.7 - - + -
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Residues in contact with CYS 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 LEU* 3.0 12.3 + - + +
105A HIS 4.3 1.1 - - - +
107A ALA* 1.3 74.0 - - - +
109A PHE* 1.3 69.4 + - - +
110A TRP 2.9 4.8 + - - -
111A GLY* 3.4 10.4 + - - +
112A GLN 4.7 4.5 - - - +
116A ALA* 5.6 4.7 - - + -
136A PRO* 3.6 42.2 - - + -
139A LYS* 3.9 26.2 - - - +
140A ALA* 5.2 4.5 - - - -
145A ARG* 5.9 4.0 - - - -
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Residues in contact with PHE 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 HIS 3.1 17.0 + - - +
106A TYR* 2.9 24.1 + + + +
108A CYS* 1.3 79.7 - - - +
110A TRP* 1.3 80.3 + + + +
139A LYS* 4.9 28.2 - - + +
12B ARG* 5.4 11.2 - - - -
37B VAL* 3.6 33.2 - - + -
39B ALA* 5.2 4.9 - - + -
42B PHE* 4.0 26.5 - + + -
57B LYS* 4.3 22.9 - - - -
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Residues in contact with TRP 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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75A ALA 4.9 3.4 - - - +
76A SER* 3.8 43.2 - - - +
77A HIS 5.4 6.3 - - - -
106A TYR* 3.2 22.8 + + - +
107A ALA 4.2 2.5 - - - +
108A CYS 3.0 1.5 - - - -
109A PHE* 1.3 102.1 - + + +
111A GLY* 1.3 58.0 + - - +
112A GLN* 4.7 11.0 - - + +
12B ARG* 5.4 10.8 - - - -
55B GLY* 3.0 37.9 - - - -
56B ARG* 4.8 7.4 - - + -
57B LYS* 5.4 3.6 - - - -
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Residues in contact with GLY 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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80A ARG* 5.6 0.5 + - - -
107A ALA 3.2 4.0 + - - -
108A CYS* 3.4 8.2 + - - -
110A TRP* 1.3 81.6 - - - +
112A GLN* 1.3 76.9 + - - +
113A ASP* 4.0 3.6 + - - +
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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