Contacts of the strand formed by residues 604 - 609 (chain A) in PDB entry 3IAY
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 ILE 604 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A TYR* 4.0 21.1 - - + -
602A VAL 3.7 9.6 - - - +
603A PRO* 1.3 81.7 - - - +
605A ALA* 1.3 62.2 + - - +
606A THR* 3.7 2.9 + - - +
759A VAL* 4.4 5.6 - - + -
767A MET* 3.6 37.0 - - + -
768A VAL 3.5 6.5 - - - +
769A LYS* 3.8 29.8 - - + +
804A ALA* 3.2 5.8 - - - -
805A TYR* 2.8 42.7 + - + +
808A TYR* 3.8 35.4 - - + -
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Residues in contact with ALA 605 (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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603A PRO 4.1 1.2 - - - -
604A ILE* 1.3 72.1 - - - +
606A THR* 1.3 60.8 + - - +
607A LEU* 3.9 2.8 + - + +
766A VAL 3.4 3.3 - - - +
767A MET* 3.5 0.9 - - - -
768A VAL* 2.8 39.0 + - + +
770A PHE* 3.7 31.4 - - + -
778A ALA* 3.9 17.9 - - + +
782A GLY* 4.2 5.6 - - - -
801A PHE* 4.0 13.9 - - + -
803A LYS 4.0 3.4 - - - -
804A ALA* 4.4 2.5 - - + +
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Residues in contact with THR 606 (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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604A ILE 3.7 1.1 + - - -
605A ALA* 1.3 72.0 - - - +
607A LEU* 1.3 61.8 + - - +
765A SER* 4.6 4.9 - - - -
766A VAL 3.5 6.5 - - - +
767A MET* 3.7 30.2 - - + +
801A PHE* 3.7 3.7 - - - -
802A GLU* 2.8 40.5 + - - +
803A LYS* 2.8 45.5 + - - +
805A TYR* 3.5 26.9 - - - -
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Residues in contact with LEU 607 (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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605A ALA* 4.6 5.8 - - + +
606A THR* 1.3 82.6 - - - +
608A ASP* 1.3 60.7 + - - +
742A VAL* 4.5 6.5 - - + -
765A SER* 3.0 6.5 - - - -
766A VAL* 2.9 52.9 + - + +
768A VAL* 4.5 12.6 - - + -
770A PHE* 5.6 0.7 - - + -
782A GLY* 3.5 30.7 - - - +
785A ALA* 4.2 11.4 - - + -
786A ALA* 4.2 13.2 - - + +
799A LEU* 3.9 28.4 - - + +
800A GLU 3.3 7.0 - - - +
801A PHE* 3.8 14.8 - - + +
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Residues in contact with ASP 608 (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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1A CA 2.4 29.1 - - - -
2A CA 3.5 9.2 - - - -
3A CA 2.6 17.0 - - - -
606A THR 4.4 0.2 + - - -
607A LEU* 1.3 76.3 - - - +
609A PHE* 1.3 61.0 + - - +
610A ASN 3.6 0.9 + - - -
764A ASP 3.2 13.7 - - - +
765A SER* 3.6 12.3 - - - -
799A LEU* 3.4 7.5 - - - +
800A GLU* 2.9 33.1 + - - +
802A GLU* 2.6 41.5 - - - +
986A DCP 3.2 0.3 + - - -
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Residues in contact with PHE 609 (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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1A CA 2.2 31.7 - - - -
608A ASP* 1.3 73.5 - - - +
610A ASN* 1.3 62.3 + - - +
612A LEU* 3.6 33.2 - - + -
615A SER* 5.6 0.2 - - - +
734A MET* 3.8 19.1 - - + -
735A ILE* 5.0 2.7 - - - -
738A THR* 3.3 29.8 - - + -
764A ASP* 3.1 34.9 + - + +
789A VAL* 4.7 0.2 - - + -
790A SER* 5.9 0.2 - - - -
793A PHE* 3.7 19.3 - + - -
797A ILE* 3.6 30.1 - - + -
798A ASN 3.4 17.9 - - - +
799A LEU* 3.7 24.9 - - + -
986A DCP 3.1 2.4 + - - -
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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
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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