Contacts of the strand formed by residues 816 - 820 (chain C) in PDB entry 2VF7
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 LEU 816 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516C LEU* 4.0 16.8 - - + +
517C ASP 3.9 10.1 - - - +
518C VAL* 3.7 33.4 - - + -
803C LEU* 3.9 19.7 - - + -
804C ASP 4.0 6.5 - - - +
805C ILE* 4.6 2.7 - - + +
815C ARG* 1.3 81.0 + - - +
817C VAL* 1.3 61.0 + - - +
818C ALA* 4.2 7.2 - - - +
819C GLN* 3.9 40.2 - - + +
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Residues in contact with VAL 817 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804C ASP* 3.0 47.8 + - - +
805C ILE 3.8 0.9 - - - -
806C GLY* 3.7 13.9 - - - +
807C PRO* 3.6 40.2 - - + -
815C ARG* 3.6 5.1 + - + -
816C LEU* 1.3 75.3 - - - +
818C ALA* 1.3 60.2 + - - +
828C ALA* 5.4 0.3 - - - +
829C ALA 4.8 8.1 - - - +
830C GLY 4.7 9.6 - - - +
831C SER* 4.6 9.2 - - - +
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Residues in contact with ALA 818 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803C LEU* 3.7 2.3 - - - -
804C ASP* 2.9 37.4 + - + +
816C LEU* 4.2 4.9 - - - +
817C VAL* 1.3 79.4 - - - +
819C GLN* 1.3 63.1 + - - +
825C VAL* 4.0 18.6 - - + -
828C ALA* 3.5 31.6 - - + -
831C SER* 4.3 5.8 - - - -
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Residues in contact with GLN 819 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ASN 5.7 0.2 - - - +
502C TRP* 5.0 1.4 - - - -
519C ARG* 3.7 36.4 + - - +
801C TRP* 4.0 23.5 + - + +
802C VAL 3.3 4.9 - - - -
803C LEU* 4.1 16.2 - - + +
816C LEU* 3.9 25.2 - - + +
818C ALA* 1.3 76.3 - - - +
820C GLY* 1.3 59.6 + - - +
824C GLU* 4.7 7.3 - - - +
825C VAL* 3.9 7.5 + - - +
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Residues in contact with GLY 820 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801C TRP* 3.6 27.4 - - - -
802C VAL* 2.4 42.0 + - - +
819C GLN* 1.3 77.5 - - - +
821C THR* 1.3 67.5 + - - +
824C GLU* 4.0 8.3 - - - -
825C VAL* 3.8 1.0 - - - +
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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