Contacts of the strand formed by residues 700 - 705 (chain D) in PDB entry 5VOT
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 TYR 700 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504D ILE* 5.4 1.7 - - - +
505D LYS 5.5 0.7 + - - -
645D ILE* 3.7 2.5 - - - -
646D ALA* 3.2 28.5 - - + -
647D TYR* 3.5 6.3 - - - -
648D GLY* 2.9 35.8 + - - -
649D THR 4.2 0.3 + - - -
681D VAL* 3.2 17.3 + - + -
683D VAL* 5.6 0.7 - - - +
692D ARG* 3.3 57.4 + - + +
693D VAL* 4.2 23.5 - - + +
696D SER* 3.4 21.9 - - - +
698D GLY* 3.2 6.0 - - - -
699D LYS* 1.3 82.4 - - + +
701D ALA* 1.3 78.4 + - - +
702D TYR* 4.2 19.2 - + - -
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Residues in contact with ALA 701 (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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502D ILE* 5.1 5.8 - - + -
503D MET 3.7 10.5 - - - +
504D ILE* 4.0 16.8 - - + -
633D ILE* 6.1 0.9 - - + -
639D LEU* 5.0 11.0 - - + -
645D ILE* 3.4 13.3 - - + +
646D ALA 2.6 13.9 + - - +
647D TYR* 3.3 22.2 - - + -
648D GLY 3.8 0.2 + - - -
700D TYR* 1.3 96.0 - - - +
702D TYR* 1.3 62.3 + - - +
703D LEU* 5.9 0.2 - - + -
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Residues in contact with TYR 702 (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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502D ILE* 3.7 1.2 - - - +
503D MET* 2.9 46.7 + - + +
648D GLY 4.5 3.6 - - - -
649D THR 5.1 4.7 - - - -
650D LEU* 4.1 16.7 - - - +
683D VAL* 4.3 11.7 - - + +
686D THR* 3.6 34.2 + - + +
689D GLY* 3.4 31.6 - - - -
690D VAL* 5.6 1.8 - - + -
693D VAL* 3.6 19.0 - - + +
700D TYR* 4.2 20.6 + + - -
701D ALA* 1.3 74.4 - - - +
703D LEU* 1.3 86.8 + - - +
704D LEU* 3.3 37.9 - - + -
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Residues in contact with LEU 703 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500D ILE* 5.4 7.4 - - + -
501D SER 3.7 3.1 - - - +
502D ILE* 3.6 35.0 - - + -
639D LEU* 5.1 7.2 - - + -
647D TYR* 3.7 33.2 - - + -
648D GLY 3.4 21.7 + - - +
649D THR* 3.7 27.4 - - + +
650D LEU* 4.8 1.4 + - - +
655D THR* 5.3 5.9 + - + +
659D PHE* 5.0 10.8 - - + -
670D MET* 4.7 9.2 - - + -
674D MET* 4.3 6.7 - - - -
701D ALA 5.8 0.2 - - - -
702D TYR* 1.3 98.5 + - - +
704D LEU* 1.3 61.6 + - - +
727D LEU* 6.5 0.4 - - + -
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Residues in contact with LEU 704 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500D ILE* 3.9 7.1 - - - +
501D SER* 2.7 51.8 + - - +
503D MET* 3.6 42.8 - - + +
655D THR* 5.5 6.1 - - - -
686D THR* 4.8 10.1 - - + -
690D VAL* 6.4 0.4 - - + -
702D TYR* 3.3 23.6 - - + +
703D LEU* 1.3 73.1 - - - +
705D GLU* 1.3 65.6 + - - +
708D MET* 3.7 13.9 - - + -
709D ASN* 3.4 31.9 - - + +
712D ILE* 5.4 1.6 - - + -
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Residues in contact with GLU 705 (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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450D TYR* 3.1 42.7 + - - -
480D THR* 3.4 16.1 + - - +
498D LEU* 4.6 8.1 - - + -
499D GLY 4.5 3.1 - - - -
500D ILE* 5.2 1.1 - - - +
501D SER* 3.0 10.4 + - - -
654D SER* 4.7 2.8 + - - +
655D THR* 5.1 9.4 + - - +
704D LEU* 1.3 78.6 - - - +
706D SER* 1.3 67.4 + - - +
707D THR 3.4 0.8 + - - +
708D MET* 3.2 20.7 + - - +
709D ASN 3.1 14.0 + - - -
732D TYR* 2.3 36.1 + - - +
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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