Contacts of the strand formed by residues 594 - 599 (chain D) in PDB entry 6V3O
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 594 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591D ILE* 3.2 31.6 + - - +
592D LYS 4.1 9.2 - - - +
593D GLY* 1.3 84.7 - - - +
595D GLN* 1.3 60.8 + - - +
633D VAL* 4.0 3.5 - - - +
634D LYS* 3.6 35.8 - - + +
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Residues in contact with GLN 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543D VAL* 5.9 0.4 - - - +
561D VAL 3.0 22.2 + - - -
563D PRO* 3.9 10.3 - - - +
578D VAL* 5.5 4.0 - - + -
581D LEU* 5.4 5.0 - - - +
582D PHE* 4.0 16.3 - - + -
587D TYR* 2.5 37.4 + - - -
591D ILE* 4.1 4.5 - - + +
594D LYS* 1.3 74.3 - - - +
596D GLN* 1.3 83.6 + - - +
597D VAL* 4.3 4.9 - - + +
633D VAL* 3.7 18.0 - - + +
634D LYS 3.2 9.5 + - - +
635D LEU* 3.3 16.2 - - + +
636D THR* 2.9 24.8 + - - -
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Residues in contact with GLN 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D PRO* 4.0 7.4 - - - +
560D PRO* 5.9 5.2 - - + +
562D VAL* 3.2 40.8 - - + +
563D PRO* 3.6 0.5 - - - +
595D GLN* 1.3 94.3 + - - +
597D VAL* 1.3 69.0 + - - +
636D THR* 3.1 25.4 - - + +
638D PHE* 3.3 21.6 - - + +
669D ARG* 2.9 44.0 + - - +
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Residues in contact with VAL 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D VAL* 3.8 4.9 - - - -
563D PRO* 3.9 9.6 - - + +
565D PHE* 3.9 25.1 - - + -
578D VAL* 4.4 11.0 - - + -
595D GLN* 4.3 7.2 - - + -
596D GLN* 1.3 81.0 - - - +
598D MET* 1.3 60.0 + - - +
599D VAL* 4.8 1.1 - - + -
624D MET* 3.8 30.7 - - + -
635D LEU* 3.6 22.9 - - + -
636D THR 2.8 5.9 + - - -
637D LEU* 3.3 19.2 - - + +
638D PHE* 2.8 31.0 + - - +
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Residues in contact with MET 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D TRP* 3.5 32.5 - - + -
456D ARG* 5.0 0.9 - - - +
533D ILE* 4.0 14.6 - - + -
562D VAL* 3.7 8.2 - - + +
563D PRO 3.1 15.5 + - - +
564D LEU* 3.6 29.2 - - + -
565D PHE* 3.3 23.6 + - - +
597D VAL* 1.3 77.1 - - - +
599D VAL* 1.3 66.7 + - - +
600D GLY* 5.7 0.4 - - - -
603D ASP* 5.9 0.9 - - - +
638D PHE* 3.3 46.0 - - + +
640D GLY* 3.7 26.0 - - - -
641D ARG 5.2 0.7 - - - +
671D THR* 4.9 0.7 - - + -
1002D SO4 5.9 1.3 - - - +
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Residues in contact with VAL 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D LEU* 4.1 4.0 - - - -
565D PHE* 4.2 5.4 - - + +
571D LEU* 3.8 19.1 - - + -
597D VAL* 4.8 3.8 - - + -
598D MET* 1.3 80.0 - - - +
600D GLY* 1.3 59.3 + - - +
601D TYR* 4.1 4.9 - - + -
617D LEU* 3.5 29.6 - - + -
620D ALA* 5.7 0.2 - - + -
621D GLN* 4.6 8.7 - - + +
624D MET* 4.6 18.4 - - + -
637D LEU* 4.9 11.2 - - + -
638D PHE 3.1 10.5 + - - +
639D HIS* 4.1 19.5 - - + +
640D GLY* 3.0 25.3 + - - -
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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