Contacts of the strand formed by residues 572 - 575 (chain A) in PDB entry 4FWF
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 HIS 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A ILE* 5.4 0.4 - - + -
439A VAL 3.3 5.4 - - - +
440A ASN* 3.1 39.2 - - + +
441A GLY* 3.8 14.9 + - - -
460A LYS* 3.7 1.9 - - - +
461A PHE* 3.0 29.6 + - + +
568A PHE 5.5 2.9 - - - -
570A GLY 3.6 7.8 + - - -
571A ASP* 1.3 73.9 - - - +
573A THR* 1.3 61.2 + - - +
3E THR* 4.8 2.2 + - - -
5E GLN 3.5 20.2 + - - -
6E THR* 4.1 22.9 - - + +
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Residues in contact with THR 573 (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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268A TYR* 3.9 6.1 - - - +
438A ILE* 3.4 5.2 - - - +
439A VAL* 2.9 40.6 + - - +
442A CYS* 3.5 23.3 - - - -
458A MET* 3.4 40.6 - - + +
459A HIS 3.0 9.0 - - - +
460A LYS* 3.9 11.7 - - + +
461A PHE* 3.8 6.0 - - - -
571A ASP* 3.7 13.5 - - + -
572A HIS* 1.3 80.4 - - - +
574A LEU* 1.3 59.5 + - - +
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Residues in contact with LEU 574 (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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437A GLN* 4.1 33.7 - - + +
438A ILE* 4.6 5.2 - - + +
458A MET* 3.5 3.6 - - - -
459A HIS* 2.6 45.7 + - + +
461A PHE* 3.6 31.1 - - + -
573A THR* 1.3 72.8 - - - +
575A LEU* 1.3 68.3 + - - +
576A THR* 3.2 16.4 + - - +
698A TYR* 6.1 0.4 - - + -
699A ASP 4.7 4.9 - - - +
700A MET* 4.5 41.5 - - + +
702A PRO* 4.7 7.6 - - + -
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Residues in contact with LEU 575 (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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437A GLN* 2.9 39.5 + - + +
439A VAL* 4.2 10.5 - - + -
447A VAL* 4.3 1.8 - - + -
451A CYS* 3.5 17.3 - - - -
456A ILE* 4.9 2.9 - - + -
457A SER 4.0 6.7 - - - +
458A MET* 3.5 28.0 - - + -
573A THR 3.8 0.4 + - - -
574A LEU* 1.3 69.9 - - - +
576A THR* 1.3 55.3 + - - +
577A PRO* 3.5 3.6 - - + -
578A GLY* 2.8 31.8 + - - +
579A TYR* 3.7 48.5 - - + +
582A ILE* 4.1 12.6 - - + -
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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