Contacts of the strand formed by residues 607 - 613 (chain A) in PDB entry 4FOV
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 ALA 607 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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597A LYS* 3.3 12.2 - - - +
598A TYR* 3.0 35.6 + - + +
600A GLN 4.5 5.3 + - - +
602A ILE* 3.7 33.7 - - + -
605A LYS 3.5 1.4 + - - +
606A GLU* 1.3 76.2 - - - +
608A VAL* 1.3 63.4 + - - +
609A ILE* 5.5 0.2 - - + -
626A VAL* 4.4 4.5 - - + -
627A GLY 3.2 9.2 - - - +
628A LEU* 3.9 9.4 - - + -
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Residues in contact with VAL 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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545A VAL* 4.2 10.8 - - + -
547A LEU* 3.6 31.4 - - + -
555A PHE* 4.0 28.7 - - + -
596A ILE 3.4 12.8 - - - +
597A LYS* 4.4 6.1 - - + -
598A TYR 4.6 0.2 - - - +
607A ALA* 1.3 78.2 - - - +
609A ILE* 1.3 76.7 + - - +
610A LEU* 4.3 1.6 - - + -
625A VAL 3.8 0.5 - - - +
626A VAL* 3.6 1.7 - - - +
627A GLY 2.8 33.1 + - - +
629A VAL* 4.3 6.7 - - + -
636A ILE* 4.1 14.1 - - + -
638A TRP* 4.4 9.2 - - + -
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Residues in contact with ILE 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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595A ALA* 3.3 4.5 - - - +
596A ILE* 2.9 41.8 + - + -
598A TYR* 4.1 18.2 - - + -
607A ALA* 5.5 0.4 - - + -
608A VAL* 1.3 79.4 - - - +
610A LEU* 1.3 72.0 + - - +
624A LEU* 4.2 21.3 - - + -
625A VAL 3.4 8.7 - - - +
626A VAL* 4.4 12.3 - - + -
656A ILE* 3.3 11.3 - - + +
664A ILE* 3.9 29.4 - - + -
692A ILE* 4.0 20.6 - - + -
695A LEU* 4.2 12.1 - - + -
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Residues in contact with LEU 610 (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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555A PHE* 3.6 26.5 - - + -
563A ILE* 4.5 5.8 - - + -
581A ILE* 3.8 28.3 - - + -
584A ILE* 4.1 17.7 - - + -
593A VAL* 4.3 15.9 - - + -
594A SER 3.3 4.0 - - - +
595A ALA* 3.6 26.0 - - + -
608A VAL* 4.3 1.1 - - + -
609A ILE* 1.3 75.7 - - - +
611A SER* 1.3 60.8 + - - +
612A THR* 4.9 2.9 - - + -
623A GLN 3.6 0.9 - - - +
624A LEU* 3.2 6.3 - - - +
625A VAL* 2.8 44.0 + - + +
638A TRP* 3.6 19.7 - - + -
656A ILE* 4.4 1.1 - - - -
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Residues in contact with SER 611 (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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593A VAL* 3.5 3.2 - - - +
594A SER* 2.7 49.7 + - - -
610A LEU* 1.3 73.2 - - - +
612A THR* 1.3 63.4 + - - +
623A GLN 3.4 4.7 - - - -
624A LEU* 3.6 6.3 - - - -
651A TYR* 2.8 22.3 + - - -
654A SER* 2.7 24.4 + - - -
656A ILE* 3.6 20.8 - - - +
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Residues in contact with THR 612 (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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563A ILE* 3.9 12.8 - - + +
584A ILE* 3.9 26.0 - - + -
586A GLN* 2.8 32.1 + - - -
592A GLN 4.7 1.6 - - - -
593A VAL* 4.3 7.9 - - + -
610A LEU* 4.9 2.5 - - + -
611A SER* 1.3 80.7 + - - +
613A PRO* 1.3 84.7 + - - +
614A ASN* 3.5 0.4 + - - -
623A GLN* 2.9 31.7 + - + +
625A VAL* 4.8 7.9 - - + -
651A TYR* 3.9 7.8 - - - -
654A SER* 4.8 0.2 - - - -
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Residues in contact with PRO 613 (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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584A ILE* 4.2 1.2 - - - +
585A GLN 3.5 9.7 - - - +
586A GLN* 4.2 6.5 - - + +
591A THR* 3.6 34.8 - - + +
592A GLN 4.5 1.6 - - - +
612A THR* 1.3 105.3 + - - +
614A ASN* 1.3 59.0 + - - +
615A SER 3.8 2.2 - - - +
618A GLY 4.7 2.7 - - - +
619A ARG* 4.3 3.6 - - - -
620A LYS 3.4 21.8 - - - +
621A GLY 3.8 3.1 - - - +
651A TYR* 3.5 23.0 - - + +
652A ALA 3.9 20.0 - - - +
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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