Contacts of the helix formed by residues 135 - 142 (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 MET 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A HIS* 3.7 4.7 - - - +
126A VAL 4.0 9.6 - - - +
127A SER* 5.0 3.1 - - - -
128A ILE* 5.8 0.4 - - + -
129A CYS* 4.1 27.1 - - - +
133A GLY* 2.4 49.7 + - - +
134A GLU* 1.3 71.7 - - - +
136A PRO* 1.3 73.4 - - + +
137A VAL* 3.4 26.7 - - + +
138A ASP* 2.8 43.8 + - - +
139A LYS* 3.3 10.0 + - - +
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Residues in contact with PRO 136 (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* 3.9 36.3 - - + +
105A HIS* 4.1 15.9 - - + +
108A CYS* 3.6 34.5 - - + -
126A VAL* 4.2 15.3 - - + +
135A MET* 1.3 89.9 - - + +
137A VAL* 1.3 52.7 + - - +
139A LYS* 3.3 3.5 - - + -
140A ALA* 2.4 41.6 + - + +
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Residues in contact with VAL 137 (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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126A VAL* 3.9 28.2 - - + +
127A SER* 4.8 7.2 - - - -
135A MET* 3.0 22.2 + - + -
136A PRO* 1.3 76.6 - - - +
138A ASP* 1.3 58.0 + - - +
140A ALA* 3.5 2.8 - - - -
141A LYS* 2.7 35.7 + - + +
149A ARG* 3.0 38.4 + - - +
152A ALA* 5.3 6.1 - - + -
153A GLU* 5.2 11.9 - - - +
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Residues in contact with ASP 138 (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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132A TYR 5.6 0.2 - - - +
133A GLY* 3.8 7.2 - - - +
134A GLU* 5.3 2.6 - - - -
135A MET* 2.8 39.0 + - - +
137A VAL* 1.3 78.9 - - - +
139A LYS* 1.3 66.7 + - - +
140A ALA 2.9 4.0 - - - -
141A LYS* 2.9 25.9 + - - +
142A ALA* 2.9 15.6 + - - +
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Residues in contact with LYS 139 (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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108A CYS* 3.9 26.2 - - - +
109A PHE* 4.9 31.6 - - + -
135A MET 3.3 4.4 + - - +
136A PRO* 3.0 10.2 + - + +
138A ASP* 1.3 80.1 - - - +
140A ALA* 1.3 56.9 + - - +
142A ALA* 4.6 6.1 - - + -
143A PRO* 2.8 24.6 - - - +
145A ARG* 4.3 2.5 + - - +
13B CYS* 5.5 11.2 - - - +
34B GLN* 4.6 15.0 + - - +
35B CYS* 6.0 2.0 - - - +
37B VAL* 5.4 4.6 - - - +
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Residues in contact with ALA 140 (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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108A CYS* 5.2 5.4 - - - -
136A PRO* 2.4 33.0 + - + +
137A VAL* 3.7 4.7 - - - +
139A LYS* 1.3 73.8 - - - +
141A LYS* 1.3 62.9 + - - +
142A ALA 3.1 2.3 + - - -
143A PRO* 3.6 6.6 - - - +
144A LEU 3.5 2.4 + - - -
145A ARG* 3.5 29.1 + - - +
148A LEU* 3.8 29.8 - - + -
149A ARG* 3.8 9.5 - - - -
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Residues in contact with LYS 141 (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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137A VAL* 2.7 19.0 + - + +
138A ASP* 2.9 15.8 + - - +
140A ALA* 1.3 78.3 - - - +
142A ALA* 1.3 63.1 + - - +
144A LEU* 3.6 24.4 + - + +
149A ARG* 3.1 27.6 - - - +
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Residues in contact with ALA 142 (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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138A ASP 2.9 13.6 + - - +
139A LYS* 4.1 6.7 - - + +
141A LYS* 1.3 79.3 - - - +
143A PRO* 1.3 77.8 - - + +
144A LEU* 2.8 7.5 + - - +
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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