Contacts of the strand formed by residues 603 - 607 (chain A) in PDB entry 4Z4Q
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 LEU 603 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A LYS* 5.4 1.8 - - + -
502A ILE* 4.2 14.6 - - + -
536A TYR* 3.7 36.3 - - + -
537A ILE 3.9 1.8 - - - +
538A ALA* 3.7 32.5 - - + +
539A LEU* 5.0 0.4 - - - -
595A THR 5.0 0.2 - - - +
601A ARG* 3.7 52.6 + - + +
602A THR* 1.3 76.0 - - - +
604A ILE* 1.3 64.1 + - - +
605A ARG 4.3 0.2 - - - -
1003A ASN 3.0 11.1 + - - +
1004A ILE* 3.5 19.5 - - + -
1005A GLN* 3.3 21.0 + - - +
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Residues in contact with ILE 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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536A TYR* 3.1 10.5 - - - +
537A ILE* 2.9 52.2 + - + +
539A LEU* 4.1 20.6 - - + -
603A LEU* 1.3 77.3 - - - +
605A ARG* 1.3 70.1 + - - +
606A VAL* 3.8 3.8 + - + +
1005A GLN* 3.4 16.4 - - + +
1007A MET* 4.1 22.0 - - + -
1012A ILE* 5.9 2.2 - - + -
1016A ARG* 4.5 22.9 - - - +
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Residues in contact with ARG 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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532A ALA 4.9 3.6 + - - -
533A GLY* 2.9 41.3 + - - +
534A HIS* 5.8 0.8 + - - -
535A VAL 4.0 2.2 - - - +
536A TYR* 3.3 36.1 + - + -
603A LEU 4.3 0.4 - - - -
604A ILE* 1.3 74.8 - - - +
606A VAL* 1.3 63.7 + - - +
607A THR* 3.5 12.0 + - - +
1004A ILE* 4.2 16.7 - - + +
1005A GLN 2.9 13.0 + - - +
1006A ASN* 3.6 27.3 + - - +
1007A MET 3.1 23.7 + - - +
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Residues in contact with VAL 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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519A LEU* 3.8 34.8 - - + -
530A VAL* 3.4 29.7 - - + +
533A GLY* 3.8 12.1 - - - -
535A VAL* 3.0 27.8 + - + +
536A TYR* 5.0 0.2 - - - -
537A ILE* 4.3 20.4 - - + -
604A ILE* 3.8 3.8 + - + +
605A ARG* 1.3 70.5 - - - +
607A THR* 1.3 66.4 + - - +
1007A MET* 3.8 4.3 - - + -
1009A LEU* 4.4 25.6 - - + -
1012A ILE* 5.2 5.6 - - + -
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Residues in contact with THR 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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530A VAL 4.3 4.0 - - - -
531A GLU 6.0 0.4 - - - -
533A GLY* 5.2 2.7 - - - -
605A ARG* 3.9 24.5 - - - +
606A VAL* 1.3 81.8 - - - +
608A ILE* 1.3 60.2 + - - +
609A GLU* 4.8 4.3 + - - +
1006A ASN* 4.0 15.4 - - + +
1007A MET 3.1 19.4 + - - -
1008A SER* 3.3 5.2 + - - -
1009A LEU* 2.8 33.5 + - - -
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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