Contacts of the strand formed by residues 124 - 128 (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 GLU 124 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131D LYS* 6.0 4.3 - - - +
122E PRO 3.9 2.2 + - - +
123E PRO* 1.3 73.7 - - - +
125E VAL* 1.3 61.1 + - - +
146E LEU 3.6 1.6 - - - +
147E ALA* 3.3 2.8 - - - -
148E THR* 2.8 62.1 + - - +
149E GLY* 4.3 6.1 - - - +
187E ARG* 4.4 10.0 + - - -
235E VAL* 4.9 1.1 - - - -
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Residues in contact with VAL 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E PRO* 4.0 7.6 + - + -
124E GLU* 1.3 79.2 - - - +
126E ALA* 1.3 64.9 + - - +
145E CYS* 3.8 25.8 - - - -
146E LEU 3.4 4.3 - - - +
147E ALA* 4.2 2.7 - - + -
210E CYS* 4.0 12.6 - - - +
212E VAL* 3.7 25.8 - - + -
235E VAL* 3.6 33.8 - - + +
236E SER 4.4 3.5 - - - +
237E ALA* 3.7 24.9 - - + +
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Residues in contact with ALA 126 (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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125D ASP* 4.0 13.7 - - - +
131D LYS* 3.8 26.0 - - - +
125E VAL* 1.3 76.1 - - - +
127E VAL* 1.3 63.8 + - - +
128E PHE* 3.9 16.7 - - + -
144E VAL 4.0 0.2 - - - +
145E CYS* 3.4 4.7 - - - -
146E LEU* 2.9 35.6 + - + +
237E ALA* 3.9 4.0 - - - -
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Residues in contact with VAL 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ASP* 3.3 4.9 + - - +
126D SER* 2.9 37.7 + - - +
126E ALA* 1.3 78.3 - - - +
128E PHE* 1.3 69.3 + - - +
129E GLU 4.1 0.2 - - - -
143E LEU* 4.0 29.6 - - + -
144E VAL 3.3 10.1 - - - +
145E CYS* 4.7 0.9 - - - -
159E TRP* 4.4 6.3 - - + -
208E PHE 5.5 0.9 - - - +
210E CYS* 3.8 18.4 - - + +
237E ALA* 3.6 34.7 - - + +
238E GLU* 4.2 5.6 - - - +
239E ALA* 4.3 10.1 - - + +
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Residues in contact with PHE 128 (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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123D LEU* 3.6 21.8 - - + +
124D ARG 3.5 2.9 - - - +
125D ASP* 3.3 39.9 - - + -
131D LYS* 4.0 17.0 - - + -
132D SER* 3.6 24.5 - - - -
133D VAL* 3.8 24.9 - - + -
126E ALA* 3.9 21.3 - - + -
127E VAL* 1.3 78.5 - - - +
129E GLU* 1.3 64.0 + - - +
143E LEU* 3.5 9.2 - - - +
144E VAL* 2.6 47.2 + - + +
146E LEU* 4.0 24.9 - - + -
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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