Contacts of the strand formed by residues 1118 - 1120 (chain E) in PDB entry 2X4X
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 VAL1118 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114E PHE* 3.3 2.6 - - - -
1115E HIS 2.7 39.3 + - - +
1116E HIS 4.1 2.5 - - - +
1117E GLY* 1.3 79.7 - - - +
1119E PRO* 1.3 80.7 - - + +
1120E ILE* 3.4 6.1 + - + +
1198E HIS* 3.9 26.9 - - + +
1201E LYS* 3.8 34.3 - - + +
1202E VAL* 3.8 20.2 - - + -
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Residues in contact with PRO1119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113E MET 3.6 8.1 - - - +
1114E PHE* 3.9 15.1 - - + -
1117E GLY 3.9 5.8 - - - +
1118E VAL* 1.3 93.9 - - + +
1120E ILE* 1.3 64.0 + - - +
1121E PRO* 3.7 7.6 - - - +
28F SER* 3.5 23.1 - - - +
29F ALA* 3.2 29.6 - - + +
30F PRO* 3.9 10.3 - - + +
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Residues in contact with ILE1120 (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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1086E LEU* 4.2 17.5 - - + -
1102E LEU* 4.5 4.0 - - + -
1104E ILE* 3.4 33.4 - - + -
1108E MET* 3.4 26.4 - - + +
1112E GLY* 4.8 0.5 - - - -
1113E MET* 3.0 35.4 + - + +
1115E HIS* 4.0 12.8 - - + -
1118E VAL* 3.6 17.7 - - + +
1119E PRO* 1.3 76.6 - - - +
1121E PRO* 1.3 72.6 - - + +
1122E VAL* 3.5 4.0 + - - +
1198E HIS* 4.3 21.3 - - + -
29F ALA* 4.1 7.4 - - - +
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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
------------------------------------------------------------
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