Contacts of the strand formed by residues 777 - 782 (chain B) in PDB entry 6X34
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 PHE 777 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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650B VAL* 2.9 24.5 + - - +
686B TRP* 3.2 41.5 - - + -
687B ALA 3.7 2.2 - - - -
688B LEU* 4.3 17.5 - - + -
712B TYR 4.0 17.7 - - - -
714B TYR* 4.1 28.5 - + - -
750B LEU* 5.3 13.4 - - + +
771B PHE* 5.0 9.2 - + - -
772B ASN 4.8 4.9 - - - -
773B LEU* 3.5 34.8 - - + -
774B ASN 5.0 0.9 - - - -
775B GLY 3.8 9.2 - - - -
776B LEU* 1.3 90.1 - - - +
778B PHE* 1.3 60.8 + - - +
1470B ARG* 5.5 6.7 - - - -
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Residues in contact with PHE 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645B ARG* 3.2 60.1 - - + -
646B PRO 5.3 1.3 - - - +
648B ILE 3.9 16.8 - - - +
649B PHE* 4.8 12.3 - + + -
650B VAL* 5.4 1.1 - - - +
686B TRP* 3.4 4.0 - - - -
687B ALA* 2.9 49.3 + - + -
688B LEU* 3.2 31.4 - - - -
689B THR* 3.5 11.9 - - - -
692B TYR* 5.2 0.7 - + - -
776B LEU* 5.1 4.5 - - + -
777B PHE* 1.3 75.6 - - - +
779B PRO* 1.3 74.8 - - + +
780B VAL* 4.7 1.8 - - + -
826B ILE* 4.1 17.7 - - + -
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Residues in contact with PRO 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B ARG* 3.5 9.0 - - - +
646B PRO* 3.3 41.9 - - + +
648B ILE* 4.6 17.9 - - + +
650B VAL* 6.1 2.2 - - + -
664B PHE* 3.5 36.3 - - + -
685B GLY 3.5 7.0 - - - +
686B TRP* 3.5 19.9 - - + -
778B PHE* 1.3 90.5 - - + +
780B VAL* 1.3 58.7 + - - +
791B PHE* 4.4 9.0 - - + -
811B CYS* 6.1 1.8 - - + -
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Residues in contact with VAL 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643B SER* 5.1 3.1 - - - -
644B ILE 3.4 12.3 - - - +
645B ARG* 4.9 0.7 - - + -
684B VAL* 3.3 6.8 - - - +
685B GLY 2.7 36.3 + - - +
687B ALA* 4.2 19.1 - - + -
692B TYR* 5.0 6.7 - - + -
707B VAL* 3.8 20.3 - - + +
778B PHE* 4.6 7.4 - - + +
779B PRO* 1.3 75.6 - - - +
781B VAL* 1.3 63.1 + - - +
791B PHE* 5.9 1.8 - - - -
826B ILE* 5.2 0.9 - - + -
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Residues in contact with VAL 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B THR 4.6 0.2 - - - -
643B SER* 3.3 5.6 - - - -
644B ILE* 3.2 42.3 + - + +
666B VAL* 6.2 2.9 - - + -
682B LEU* 5.4 4.5 - - + -
683B ARG 3.7 12.1 - - - +
684B VAL* 4.2 16.4 - - + +
707B VAL* 4.7 1.1 - - - -
780B VAL* 1.3 76.5 - - - +
782B SER* 1.3 73.3 + - - +
783B PHE* 4.4 6.9 + - + -
789B VAL* 4.6 29.6 - - + -
791B PHE* 4.9 18.8 - - + -
1628B VAL* 6.0 2.2 - - + -
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Residues in contact with SER 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641B VAL* 5.7 0.9 - - - -
642B THR 3.5 17.6 + - - -
643B SER* 4.1 0.7 - - - -
681B HIS* 3.6 24.1 - - - +
682B LEU* 3.6 6.8 - - - +
683B ARG* 3.0 27.4 + - - +
692B TYR* 3.9 4.3 + - - -
706B GLY* 4.2 3.9 - - - -
707B VAL* 3.3 38.9 + - - +
781B VAL* 1.3 76.0 - - - +
783B PHE* 1.3 61.5 + - - +
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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