Contacts of the strand formed by residues 849 - 853 (chain A) in PDB entry 6QVC
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 ALA 849 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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826A PHE* 3.6 8.5 - - + -
828A LEU* 4.6 15.3 - - + -
837A THR* 6.2 0.2 - - + -
840A LEU* 6.2 0.9 - - + -
841A PHE* 3.5 20.9 - - + -
848A LEU* 1.3 77.0 - - - +
850A TYR* 1.3 63.1 + - - +
851A VAL* 3.7 8.9 + - + -
860A VAL* 3.3 10.0 - - - +
861A LEU* 2.9 47.9 + - + +
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Residues in contact with TYR 850 (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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614A LYS* 3.8 25.5 + - + -
636A THR* 5.6 4.2 + - - +
637A LEU 5.4 0.7 - - - -
638A PRO* 4.2 26.8 - - + +
648A LEU* 3.7 31.6 - - + -
824A SER* 5.6 2.5 - - - -
826A PHE* 3.4 33.1 - + + +
827A GLN* 4.0 8.5 - - - -
828A LEU* 3.6 16.5 + - - +
848A LEU* 5.8 9.3 - - + +
849A ALA* 1.3 72.9 - - - +
851A VAL* 1.3 60.2 + - - +
852A THR* 3.7 4.4 + - + +
857A LEU* 3.7 31.0 - - + -
859A GLY 3.9 2.5 - - - -
860A VAL* 4.4 13.7 - - + -
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Residues in contact with VAL 851 (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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609A MET* 3.7 24.9 - - + -
828A LEU* 3.6 44.0 - - + +
830A GLU* 3.7 20.2 - - + +
849A ALA* 4.0 10.3 - - + +
850A TYR* 1.3 70.8 - - - +
852A THR* 1.3 60.9 + - - +
857A LEU* 3.5 0.8 - - - +
858A ARG* 2.8 24.8 + - - +
859A GLY* 2.9 35.2 + - - +
861A LEU* 4.2 17.5 - - + -
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Residues in contact with THR 852 (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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648A LEU* 4.8 9.4 - - + -
827A GLN* 2.4 45.8 + - + +
828A LEU 3.3 16.6 + - - +
829A VAL* 5.0 1.6 - - - -
830A GLU* 3.2 15.8 - - - +
850A TYR* 3.7 10.2 + - + +
851A VAL* 1.3 75.6 - - - +
853A SER* 1.3 59.3 + - - +
855A GLY* 3.4 23.4 + - - +
856A LYS 3.3 14.4 - - - -
857A LEU* 3.7 19.1 - - + -
858A ARG 4.0 0.2 - - - +
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Residues in contact with SER 853 (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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827A GLN* 4.9 0.7 - - - +
830A GLU* 3.3 24.1 + - - -
852A THR* 1.3 71.0 - - - +
854A MET* 1.3 77.4 + - - +
855A GLY 3.2 1.1 - - - -
856A LYS* 3.0 31.1 + - - +
858A ARG* 3.7 7.0 - - - +
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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