Contacts of the strand formed by residues 602 - 605 (chain A) in PDB entry 2FO1
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 THR 602 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A GLU* 3.9 7.4 + - - +
601A THR* 1.3 82.5 + - - +
603A PHE* 1.3 66.4 + - - +
604A ARG* 3.4 15.3 + - + +
609A LEU* 3.4 5.2 - - - -
610A HIS* 3.0 40.7 + - + -
611A CYS* 5.8 0.2 - - - -
67D GLU* 5.2 6.5 + - - +
70D HIS* 4.0 21.3 - - + +
71D ARG* 4.5 12.9 - - - +
74D SER* 3.7 19.8 + - - -
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Residues in contact with PHE 603 (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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586A PHE 2.9 26.2 - - - -
587A LYS 4.2 0.4 - - - -
588A PRO* 3.2 50.3 - - + -
601A THR* 4.5 1.7 - - + +
602A THR* 1.3 72.2 - - - +
604A ARG* 1.3 75.2 + - - +
605A SER* 3.0 29.6 - - - -
606A GLU* 3.4 8.5 - - + -
609A LEU* 4.0 18.4 - - + -
70D HIS 4.9 0.5 - - - +
73D ARG* 4.7 1.7 - - - +
74D SER* 3.2 31.2 + - - +
77D ALA* 4.3 17.7 - - + +
78D ARG* 4.1 6.6 - - - +
1217E VAL* 4.8 4.3 - - + -
1251E GLU* 4.1 8.5 - - - -
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Residues in contact with ARG 604 (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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602A THR* 4.1 15.9 - - + +
603A PHE* 1.3 95.0 + - - +
605A SER* 1.3 63.9 + - - +
608A SER* 3.3 16.4 + - - +
610A HIS* 3.7 36.0 - - + -
70D HIS* 3.0 54.5 + - - +
73D ARG* 5.2 7.6 - - - +
77D ALA* 5.8 0.2 - - - +
1172E HIS* 3.3 36.8 + - + +
1173E ASN* 4.6 0.2 - - - +
1174E GLU* 4.7 2.4 + - - +
1217E VAL* 3.2 38.0 + - + +
1218E SER 4.2 15.8 + - - -
1219E ASN* 5.4 0.6 - - - +
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Residues in contact with SER 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A PHE* 4.2 0.5 - - - +
603A PHE* 3.0 16.4 - - - -
604A ARG* 1.3 79.5 - - - +
606A GLU* 1.3 60.1 + - - +
607A GLU* 2.8 22.5 + - - +
608A SER* 3.1 30.4 + - - +
1172E HIS* 4.6 4.8 - - - -
1216E GLN* 3.5 38.4 + - - -
1217E VAL* 4.2 3.8 - - - -
1251E GLU* 3.5 5.8 - - - -
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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