Contacts of the strand formed by residues 622 - 625 (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 LYS 622 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A LYS* 3.7 31.4 - - + +
384A SER 3.2 9.5 + - - +
385A VAL* 3.4 13.9 - - + -
386A ILE* 3.2 21.7 + - - +
608A VAL* 4.1 3.5 - - - +
620A ALA* 3.8 5.0 - - - +
621A GLN* 1.3 89.6 + - + +
623A VAL* 1.3 62.2 + - - +
788A GLY 2.7 26.3 + - - +
789A THR* 3.5 13.2 - - - +
791A PHE* 3.7 23.6 - - + -
818A LYS 5.7 0.2 - - - -
819A ILE* 3.7 24.9 - - + +
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Residues in contact with VAL 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 4.6 1.6 - - - -
386A ILE* 3.3 23.1 - - + +
388A ILE* 3.7 27.8 - - + -
601A ILE* 4.1 9.6 - - + -
608A VAL* 3.5 26.2 - - + -
610A VAL* 4.3 7.0 - - + -
622A LYS* 1.3 75.6 - - - +
624A LEU* 1.3 64.8 + - - +
625A VAL 4.1 0.9 - - - +
789A THR 2.8 11.3 + - - +
790A VAL* 3.6 29.8 - - + -
791A PHE* 2.8 29.7 + - - -
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Residues in contact with LEU 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 4.6 0.9 - - + +
386A ILE 2.9 14.2 + - - +
387A ILE* 3.6 17.0 - - + -
388A ILE 2.8 29.0 + - - +
397A ALA* 3.4 33.4 - - + -
623A VAL* 1.3 75.8 - - - +
625A VAL* 1.3 59.3 + - - +
626A THR* 3.6 15.1 + - + +
791A PHE* 3.4 26.5 - - + +
792A PHE 3.8 2.2 - - - +
793A ALA* 3.5 29.4 - - + +
815A GLU* 3.9 13.2 - - + -
819A ILE* 4.3 15.9 - - + -
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Residues in contact with VAL 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ILE* 4.2 6.7 - - + -
601A ILE* 3.9 14.6 - - + -
623A VAL* 5.2 1.6 - - + -
624A LEU* 1.3 72.3 - - - +
626A THR* 1.3 61.5 + - - +
627A VAL* 3.7 32.3 - - + +
632A LEU* 4.4 2.5 - - + -
637A ILE* 4.8 5.4 - - + -
639A PHE* 3.8 35.4 - - + -
790A VAL* 4.2 7.6 - - + -
791A PHE 2.9 7.7 + - - +
792A PHE* 3.5 28.3 - - + +
793A ALA 3.0 25.1 + - - +
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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