Contacts of the strand formed by residues 801 - 805 (chain A) in PDB entry 2VF8
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 TRP 801 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A PRO* 5.4 7.9 - - + -
502A TRP* 3.7 35.0 - + - -
519A ARG 4.4 4.6 + - - -
521A PRO* 3.4 36.3 - - + +
524A VAL* 4.7 0.9 - - + -
525A MET 3.0 5.9 + - - +
526A THR* 3.3 5.1 - - + +
527A SER 3.1 22.3 + - - -
799A SER* 3.5 3.4 - - - -
800A ASP* 1.3 83.9 - - - +
802A VAL* 1.3 75.5 + - - +
803A LEU* 3.9 18.5 - - + +
819A GLN* 4.1 19.1 + - + +
820A GLY* 3.4 44.4 - - - +
821A THR* 3.7 11.9 - - + +
822A PRO* 4.5 0.4 - - - +
824A GLU* 4.4 7.9 - - - -
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Residues in contact with VAL 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A SER 3.2 11.2 - - - +
529A THR* 3.9 27.8 - - + +
796A VAL* 4.0 15.5 - - + -
799A SER* 4.5 2.2 - - - -
801A TRP* 1.3 80.2 - - - +
803A LEU* 1.3 74.2 + - - +
819A GLN* 3.3 5.2 - - - +
820A GLY 2.9 35.6 + - - +
822A PRO* 3.7 32.3 - - + -
825A VAL* 4.2 22.2 - - + -
837A LEU* 4.9 1.6 - - + -
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Residues in contact with LEU 803 (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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518A VAL* 4.2 25.4 - - + -
519A ARG 4.3 13.2 - - - +
520A PHE* 4.5 16.2 - - + -
526A THR* 3.5 27.8 - - + -
527A SER 3.0 9.4 + - - +
528A VAL* 3.5 9.1 - - + -
529A THR* 3.0 26.3 + - - +
539A LEU* 4.9 2.9 - - + -
801A TRP* 3.9 9.6 - - + -
802A VAL* 1.3 81.3 - - - +
804A ASP* 1.3 59.7 + - - +
805A ILE* 3.2 20.1 - - + +
816A LEU* 4.6 6.1 - - + -
818A ALA 3.5 5.8 - - - +
819A GLN* 4.2 17.3 - - + +
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Residues in contact with ASP 804 (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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529A THR* 2.6 27.1 + - - +
530A GLY* 4.6 0.4 - - - -
802A VAL* 4.3 1.2 - - - +
803A LEU* 1.3 71.4 - - - +
805A ILE* 1.4 66.5 + - - +
807A PRO 5.8 0.3 - - - +
816A LEU* 3.8 3.6 - - - +
817A VAL* 2.8 40.7 + - + +
818A ALA* 2.8 20.7 + - + +
825A VAL* 4.9 6.3 - - + -
831A SER* 2.8 31.2 - - - -
832A VAL 3.8 1.0 + - - -
833A THR* 2.6 34.8 + - - +
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Residues in contact with ILE 805 (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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513A LEU* 5.0 4.5 - - + -
516A LEU* 5.8 5.2 - - + -
518A VAL* 6.3 0.4 - - + -
528A VAL* 3.6 16.4 - - + -
529A THR 3.0 14.5 + - - +
530A GLY* 4.1 5.2 - - - -
531A VAL 4.5 0.5 + - - -
534A SER* 3.1 44.2 + - - +
535A GLY* 3.8 13.2 - - - +
536A LYS 4.7 3.6 - - - +
539A LEU* 4.1 20.2 - - + -
803A LEU* 3.2 39.5 - - + +
804A ASP* 1.4 80.6 - - - +
806A GLY* 1.4 65.2 + - - +
807A PRO* 4.0 6.4 - - - +
814A GLY* 4.8 5.6 - - - +
815A ARG 3.5 8.3 - - - +
816A LEU* 5.1 7.6 - - + -
817A VAL* 4.1 6.3 - - - +
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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