Contacts of the strand formed by residues 594 - 599 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591H ILE* 3.1 30.5 + - - +
592H LYS 4.0 9.4 - - - +
593H GLY* 1.3 85.3 - - - +
595H GLN* 1.3 61.0 + - - +
633H VAL* 4.0 3.0 - - - +
634H LYS* 3.6 26.2 - - + +
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Residues in contact with GLN 595 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543H VAL* 5.7 0.6 - - - +
561H VAL 3.1 21.2 + - - -
563H PRO* 3.9 10.1 - - - +
578H VAL* 5.4 2.7 - - + -
581H LEU* 5.8 4.9 - - - +
582H PHE* 3.9 29.4 - - + -
587H TYR* 2.4 37.3 + - - -
591H ILE* 4.1 5.1 - - + +
594H LYS* 1.3 74.5 - - - +
596H GLN* 1.3 85.6 + - - +
597H VAL* 4.3 11.1 - - + +
633H VAL* 3.7 4.8 - - + +
634H LYS 3.1 9.9 + - - +
635H LEU* 3.2 8.7 - - + +
636H THR* 2.9 23.3 + - - -
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Residues in contact with GLN 596 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531H PRO* 4.0 15.4 - - - +
560H PRO* 5.9 4.4 - - + +
561H VAL 5.1 0.4 + - - -
562H VAL* 3.5 34.6 - - + +
563H PRO* 3.5 1.7 - - - +
595H GLN* 1.3 94.1 + - - +
597H VAL* 1.3 70.0 + - - +
636H THR* 3.2 26.8 - - + +
638H PHE* 3.3 26.7 - - + +
669H ARG* 3.2 37.8 + - - +
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Residues in contact with VAL 597 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562H VAL* 3.9 5.4 - - - -
563H PRO* 3.8 13.2 - - + +
565H PHE* 3.8 32.8 - - + -
578H VAL* 4.5 8.7 - - + -
595H GLN* 4.3 8.7 - - + +
596H GLN* 1.3 81.9 - - - +
598H MET* 1.3 67.7 + - - +
599H VAL* 4.7 2.5 - - + -
624H MET* 4.0 20.6 - - + -
635H LEU* 3.7 20.6 - - + -
636H THR 2.9 5.5 + - - -
637H LEU* 3.4 18.2 - - + +
638H PHE* 2.9 23.8 + - - +
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Residues in contact with MET 598 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288H TRP* 3.5 31.9 - - + -
456H ARG* 5.0 0.7 - - - +
533H ILE* 4.1 14.6 - - + -
562H VAL* 3.8 8.6 - - + +
563H PRO 3.0 21.1 + - - +
564H LEU* 3.7 29.2 - - + -
565H PHE* 3.3 16.3 + - - +
597H VAL* 1.3 75.0 - - - +
599H VAL* 1.3 71.0 + - - +
600H GLY* 5.7 0.7 - - - -
603H ASP* 5.9 0.9 - - - +
638H PHE* 3.3 44.9 - - + +
640H GLY* 3.7 26.9 - - - -
641H ARG 5.1 0.9 - - - +
671H THR* 4.9 0.2 - - - +
1003H SO4 5.7 2.2 - - - +
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Residues in contact with VAL 599 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564H LEU* 4.1 3.8 - - - -
565H PHE* 4.2 5.8 - - + -
571H LEU* 4.5 12.8 - - + -
597H VAL* 4.7 5.6 - - + -
598H MET* 1.3 81.5 - - - +
600H GLY* 1.3 58.7 + - - +
601H TYR* 4.2 14.7 - - + +
617H LEU* 3.5 31.2 - - + -
620H ALA* 6.2 0.2 - - + -
621H GLN* 4.9 7.0 - - + +
624H MET* 4.6 18.6 - - + -
637H LEU* 4.9 11.0 - - + -
638H PHE 3.1 11.0 + - - +
639H HIS* 4.3 13.7 - - + +
640H GLY* 3.0 25.5 + - - -
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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