Contacts of the helix formed by residues 139 - 151 (chain A) in PDB entry 2KWI
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 PRO 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A HIS* 5.6 1.1 - - + -
136A ARG* 3.9 19.5 - - - +
137A GLN 4.1 5.4 - - - +
138A VAL* 1.3 84.5 - - - +
140A VAL* 1.3 63.1 + - - +
141A GLU* 3.0 18.8 + - + +
142A GLU* 3.2 44.0 - - + +
143A ALA* 3.3 6.5 + - - +
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Residues in contact with VAL 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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95A ILE* 4.4 21.3 - - + -
136A ARG* 4.2 14.5 - - - +
138A VAL 3.5 0.4 + - - -
139A PRO* 1.3 70.7 - - - +
141A GLU* 1.3 55.7 + - - +
143A ALA* 3.6 7.2 - - - -
144A ARG* 2.7 66.7 + - + +
154A TYR* 3.5 20.0 - - + -
156A GLU* 4.3 26.7 - - + +
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Residues in contact with GLU 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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139A PRO* 3.0 11.8 - - + +
140A VAL* 1.3 77.9 - - - +
142A GLU* 1.3 58.9 + - + +
144A ARG* 3.9 8.3 - - - +
145A SER* 3.1 24.0 + - - -
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Residues in contact with GLU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A HIS* 4.7 7.7 + - - -
101A PHE* 3.4 31.3 - - + -
138A VAL* 3.7 5.0 - - + +
139A PRO* 3.2 37.4 + - + +
141A GLU* 1.3 78.0 - - - +
143A ALA* 1.3 65.2 + - - +
145A SER* 3.2 10.5 + - - -
146A LYS* 2.8 34.9 + - + +
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Residues in contact with ALA 143 (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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93A PHE* 4.3 5.2 - - + -
95A ILE* 5.8 1.6 - - + -
101A PHE* 3.7 22.7 - - + -
125A VAL* 6.0 0.3 - - - +
138A VAL* 5.4 1.6 - - + -
139A PRO 3.3 8.9 + - - +
140A VAL* 3.1 14.1 + - - +
142A GLU* 1.3 82.8 - - - +
144A ARG* 1.3 60.4 + - - +
146A LYS* 3.2 13.2 + - - +
147A ALA* 3.2 10.7 + - - +
154A TYR* 3.9 34.6 - - + +
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Residues in contact with ARG 144 (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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140A VAL* 2.7 48.8 + - + +
141A GLU* 3.9 7.2 - - - +
143A ALA* 1.3 69.2 - - - +
145A SER* 1.3 64.6 + - - +
147A ALA* 3.1 12.6 + - + +
148A GLU* 3.1 19.6 + - - +
154A TYR* 3.7 15.7 - - + +
156A GLU* 5.3 5.5 + - - -
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Residues in contact with SER 145 (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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141A GLU 3.1 16.6 + - - -
142A GLU* 3.3 15.7 - - - -
144A ARG* 1.3 77.1 - - - +
146A LYS* 1.3 50.5 + - - +
148A GLU* 3.2 15.1 + - - +
149A GLU* 2.7 33.2 + - - +
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Residues in contact with LYS 146 (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 PHE* 3.8 28.0 - - + -
104A THR* 5.8 2.2 - - - +
125A VAL* 6.2 2.5 - - + -
142A GLU* 2.8 20.2 + - - +
143A ALA* 3.3 10.1 - - - +
144A ARG 3.2 0.2 - - - -
145A SER* 1.3 73.8 - - - +
147A ALA* 1.3 63.9 + - - +
149A GLU* 2.7 42.8 + - - +
150A TRP* 2.9 50.3 + - + +
152A VAL* 5.1 0.2 - - - -
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Residues in contact with ALA 147 (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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125A VAL* 5.7 2.9 - - + +
143A ALA 3.2 3.0 + - - +
144A ARG* 3.1 11.6 + - + +
146A LYS* 1.3 78.8 - - - +
148A GLU* 1.3 57.6 + - - +
151A GLY 2.8 8.0 + - - -
152A VAL* 2.7 54.9 + - + +
153A GLN* 3.9 2.7 - - - +
154A TYR* 3.7 33.7 - - + +
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Residues in contact with GLU 148 (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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144A ARG 3.1 11.6 + - - +
145A SER* 3.2 17.0 + - - +
147A ALA* 1.3 73.0 - - - +
149A GLU* 1.3 65.3 + - - +
151A GLY* 3.2 12.5 + - - +
152A VAL 4.9 1.1 - - - -
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Residues in contact with GLU 149 (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 ARG* 5.1 0.7 + - - -
145A SER 2.7 18.1 + - - +
146A LYS* 2.7 44.8 + - - +
148A GLU* 1.3 75.6 - - - +
150A TRP* 1.3 83.4 + - + +
151A GLY 3.7 0.2 + - - -
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Residues in contact with TRP 150 (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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91A LEU* 3.7 25.1 - - + -
104A THR* 3.7 36.1 - - - -
105A ALA* 4.4 12.1 - - + -
108A ARG* 3.4 58.9 + - - +
123A LEU* 4.9 8.5 - - + -
125A VAL* 4.1 18.8 - - + -
146A LYS* 2.9 33.9 + - + +
149A GLU* 1.3 109.9 + - + +
151A GLY* 1.3 62.8 + - - +
152A VAL* 3.3 22.4 - - + +
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Residues in contact with GLY 151 (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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147A ALA 2.8 5.6 + - - -
148A GLU* 3.2 12.4 + - - -
149A GLU 3.4 0.2 - - - -
150A TRP* 1.3 80.7 - - - +
152A VAL* 1.3 62.9 + - - +
153A GLN* 5.2 0.3 - - - +
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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