Contacts of the strand formed by residues 4145 - 4150 (chain A) in PDB entry 4O2W
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 HIS4145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4093A HIS* 3.6 1.5 + - - -
4113A LYS* 4.1 2.9 - - - +
4142A GLY* 2.7 34.9 + - - +
4143A PHE 3.8 0.2 - - - -
4144A LYS* 1.3 80.6 + - - +
4146A SER* 1.3 66.8 + - - +
4147A ALA* 5.6 0.7 - - + -
4157A THR* 5.6 1.8 - - + -
4158A PHE 3.3 14.6 - - - +
4160A ASN 4.0 7.0 - - - +
4165A ARG* 3.6 34.6 + - + +
4166A LEU* 3.8 16.2 - - + -
4193A CYS* 3.6 27.5 - - + +
4194A GLY 3.7 21.0 + - - -
4195A LEU 4.7 0.6 + - - -
4196A ASN* 4.7 0.9 - - - -
4197A HIS 3.9 9.6 - - - -
4198A THR* 3.0 26.1 + - + -
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Residues in contact with SER4146 (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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4093A HIS* 2.7 29.4 + - - -
4095A MET* 3.7 21.5 - - - -
4113A LYS 2.8 21.4 + - - -
4140A SER 3.5 6.7 - - - -
4142A GLY 4.5 0.2 - - - +
4145A HIS* 1.3 75.9 - - - +
4147A ALA* 1.3 65.9 + - - +
4157A THR* 3.5 2.9 - - - -
4158A PHE* 2.9 42.3 + - - +
4193A CYS* 4.4 3.4 - - - -
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Residues in contact with ALA4147 (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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4095A MET* 3.7 1.4 - - - +
4139A MET* 3.4 0.5 - - - -
4140A SER 2.9 30.6 + - - +
4146A SER* 1.3 78.2 - - - +
4148A VAL* 1.3 69.7 + - - +
4155A LEU* 4.3 0.7 - - + -
4156A PHE 3.2 13.0 - - - +
4157A THR* 3.9 11.9 - - + -
4158A PHE* 4.5 1.5 - - - -
4191A VAL* 3.8 22.2 - - + -
4193A CYS* 3.7 20.6 - - - -
4198A THR* 5.2 0.2 - - + -
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Residues in contact with VAL4148 (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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4095A MET* 4.1 21.1 - - - -
4103A VAL* 4.5 8.5 - - + -
4131A LEU* 4.0 27.6 - - + -
4136A VAL* 4.0 20.2 - - + -
4138A GLN 3.5 4.9 - - - -
4139A MET* 4.3 12.3 - - + +
4147A ALA* 1.3 80.1 - - - +
4149A VAL* 1.3 63.8 + - - +
4150A THR* 5.4 0.2 - - + -
4154A LYS 3.9 0.3 - - - +
4155A LEU* 3.4 6.1 - - - +
4156A PHE* 3.0 56.0 + - + +
4158A PHE* 4.5 7.0 - - + -
4191A VAL* 4.6 0.2 - - - -
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Residues in contact with VAL4149 (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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4136A VAL* 3.5 5.2 - - - +
4137A VAL* 2.8 31.3 + - + -
4138A GLN* 2.9 34.0 + - + +
4148A VAL* 1.3 77.2 - - - +
4150A THR* 1.3 69.9 + - - +
4154A LYS 3.3 6.7 - - - +
4155A LEU* 3.9 4.3 - - + -
4188A ILE* 3.2 46.7 - - + +
4189A GLY* 3.8 13.7 - - - +
4190A GLN 4.0 4.9 - - - -
4191A VAL* 3.8 12.3 - - + -
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Residues in contact with THR4150 (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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4131A LEU* 5.7 0.2 - - + -
4134A GLU* 3.7 29.2 - - + +
4135A GLU 3.3 10.5 - - - +
4136A VAL* 4.2 6.5 - - + +
4137A VAL* 3.9 5.5 - - - +
4148A VAL* 5.4 0.7 - - + -
4149A VAL* 1.3 83.0 - - - +
4151A SER* 1.3 58.8 + - - +
4152A ASP* 2.4 26.4 + - - -
4153A GLY* 2.9 20.6 + - - -
4154A LYS* 3.0 24.9 + - - +
4156A PHE* 3.8 27.8 - - + -
4188A ILE 4.3 0.7 - - - +
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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