Contacts of the helix formed by residues 131 - 139 (chain E) in PDB entry 2VLK
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 131 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D TYR* 3.4 25.0 - - - +
122D GLN 3.2 26.7 - - - -
123D LEU* 4.7 2.6 - - - +
124D ARG* 4.7 5.2 - - - +
129E GLU 3.8 0.4 + - - -
130E PRO* 1.3 74.8 - - - +
132E GLU* 1.3 82.8 + - - +
133E ALA* 3.2 1.8 + - - -
134E GLU* 3.2 21.2 + - - +
135E ILE* 3.2 16.4 + - - +
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Residues in contact with GLU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D GLN 5.5 0.2 - - - +
124D ARG* 5.3 6.8 + - - +
200D PRO* 5.5 0.9 - - - +
201D SER 4.4 11.6 - - - +
130E PRO 4.0 1.2 + - - -
131E SER* 1.3 81.6 - - - +
133E ALA* 1.3 78.2 + - + +
135E ILE* 3.3 11.6 + - - +
136E SER* 2.9 29.5 + - - -
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Residues in contact with ALA 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D TYR* 3.8 8.1 - - + -
198D PHE* 4.7 4.6 - - + -
200D PRO* 3.7 35.4 - - + -
131E SER* 3.2 1.5 + - - +
132E GLU* 1.3 92.1 - - + +
134E GLU* 1.3 55.3 + - - +
136E SER* 3.6 7.5 + - - +
137E HIS* 2.6 38.5 + - - +
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Residues in contact with GLU 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D TYR* 3.3 42.0 - - + +
123D LEU* 6.0 1.0 - - - +
135D LEU* 4.9 3.5 - - - +
137D THR* 5.1 0.7 - - - +
130E PRO* 3.8 10.2 - - - +
131E SER* 3.2 16.2 + - - +
133E ALA* 1.3 75.5 - - - +
135E ILE* 1.3 55.6 + - - +
137E HIS* 3.0 1.7 + - - -
138E THR* 2.8 44.1 + - - +
140E LYS 3.4 14.6 - - - +
141E ALA* 3.6 3.1 - - - -
142E THR* 2.7 46.8 + - - +
195E ARG* 3.1 21.8 + - - +
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Residues in contact with ILE 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E PRO* 4.5 7.4 - - + +
131E SER 3.2 15.8 + - - +
132E GLU* 3.3 12.3 - - - +
134E GLU* 1.3 77.7 - - - +
136E SER* 1.3 62.2 + - - +
139E GLN* 2.8 35.5 + - - +
140E LYS 3.6 19.1 - - - +
141E ALA* 4.1 11.9 - - + -
198E ALA* 4.2 17.5 - - + -
201E TRP* 3.6 33.7 - - + +
202E GLN* 4.2 22.2 - - + +
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Residues in contact with SER 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E GLU 2.9 19.1 + - - -
133E ALA* 3.8 7.6 + - - -
135E ILE* 1.3 78.3 - - - +
137E HIS* 1.3 62.8 + - - +
138E THR 3.7 0.2 + - - -
139E GLN* 4.8 10.5 + - - +
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Residues in contact with HIS 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ASP* 3.0 43.7 + - - +
119D ALA* 5.1 0.7 - - + -
121D TYR* 3.7 20.4 - - - +
198D PHE* 3.8 37.9 - + + +
133E ALA 2.6 22.3 + - - +
134E GLU 3.7 2.5 - - - +
136E SER* 1.3 77.5 + - - +
138E THR* 1.3 62.4 + - + +
139E GLN* 5.9 0.2 - - - -
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Residues in contact with THR 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ASP* 5.2 8.7 - - + +
121D TYR* 4.0 16.2 - - - +
138D ASP* 4.2 15.7 - - - +
134E GLU* 2.8 21.4 + - + +
137E HIS* 1.3 87.1 - - + +
139E GLN* 1.3 69.4 + - - +
140E LYS* 3.1 44.2 + - - +
195E ARG* 3.6 11.1 + - - +
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Residues in contact with GLN 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D MET* 5.0 5.3 - - + +
135E ILE* 2.8 33.2 + - - +
136E SER* 4.8 8.9 - - - +
137E HIS 5.9 0.2 - - - -
138E THR* 1.3 73.6 - - - +
140E LYS* 1.3 60.5 + - - +
197E SER* 4.0 5.0 - - - -
198E ALA* 3.1 43.2 + - - +
199E THR* 6.1 1.0 - - - +
202E GLN* 5.4 2.0 + - - -
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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