Contacts of the strand formed by residues 777 - 782 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650H VAL* 2.9 26.9 + - - +
686H TRP* 3.2 43.3 - - + -
687H ALA 3.7 2.7 - - - -
688H LEU* 4.3 17.7 - - + -
712H TYR 4.0 17.5 - - - -
714H TYR* 4.1 26.0 - + - -
750H LEU* 5.3 13.6 - - + +
771H PHE* 5.0 9.0 - + - -
772H ASN 4.8 4.9 - - - -
773H LEU* 3.5 36.3 - - + -
774H ASN 5.0 0.4 - - - -
775H GLY* 3.8 9.4 - - - -
776H LEU* 1.3 88.6 - - - +
778H PHE* 1.3 59.8 + - - +
1470H ARG* 5.5 7.2 - - - -
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Residues in contact with PHE 778 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645H ARG* 3.2 62.6 - - + -
646H PRO 5.3 1.1 - - - +
648H ILE 3.9 16.2 - - - +
649H PHE* 4.8 12.8 - + + -
650H VAL* 5.4 1.1 - - - +
686H TRP* 3.4 4.4 - - - -
687H ALA* 2.9 50.4 + - + -
688H LEU 3.2 31.0 - - - -
689H THR* 3.5 11.9 - - - -
692H TYR* 5.2 1.6 - + - -
776H LEU* 5.1 3.8 - - + -
777H PHE* 1.3 76.0 - - - +
779H PRO* 1.3 75.8 - - + +
780H VAL* 4.7 2.0 - - + -
826H ILE* 4.1 16.8 - - + -
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Residues in contact with PRO 779 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645H ARG* 3.5 9.2 - - - +
646H PRO* 3.3 43.0 - - + +
648H ILE* 4.6 18.2 - - + +
650H VAL* 6.1 2.2 - - + -
664H PHE* 3.5 37.2 - - + -
685H GLY 3.5 7.0 - - - +
686H TRP* 3.5 20.6 - - + -
777H PHE 4.5 0.2 - - - +
778H PHE* 1.3 86.8 - - + +
780H VAL* 1.3 58.9 + - - +
791H PHE* 4.4 9.4 - - + -
811H CYS* 6.1 1.6 - - + -
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Residues in contact with VAL 780 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643H SER* 5.1 3.4 - - - -
644H ILE 3.4 12.6 - - - +
645H ARG* 4.9 0.4 - - + -
684H VAL* 3.3 6.0 - - - +
685H GLY 2.7 37.1 + - - +
687H ALA* 4.2 18.2 - - + -
692H TYR* 5.0 6.5 - - + -
707H VAL* 3.8 21.3 - - + -
778H PHE* 4.6 7.2 - - + +
779H PRO* 1.3 76.2 - - - +
781H VAL* 1.3 62.1 + - - +
791H PHE* 5.9 2.0 - - - -
826H ILE* 5.2 0.9 - - + -
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Residues in contact with VAL 781 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643H SER* 3.3 6.0 - - - -
644H ILE* 3.2 43.3 + - + +
666H VAL* 6.2 3.1 - - + -
682H LEU* 5.4 4.9 - - + -
683H ARG 3.7 11.0 - - - +
684H VAL* 4.2 16.6 - - + -
707H VAL* 4.7 0.7 - - - -
780H VAL* 1.3 77.2 - - - +
782H SER* 1.3 72.4 + - - +
783H PHE* 4.4 8.1 + - + -
789H VAL* 4.6 29.2 - - + -
791H PHE* 4.9 17.7 - - + -
1628H VAL* 6.0 2.0 - - + -
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Residues in contact with SER 782 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641H VAL* 5.7 0.9 - - - -
642H THR 3.5 17.2 + - - -
643H SER* 4.1 0.7 - - - -
681H HIS* 3.6 23.2 - - - +
682H LEU* 3.6 7.3 - - - +
683H ARG* 3.0 27.1 + - - +
692H TYR* 3.9 4.0 + - - -
706H GLY* 4.2 4.1 - - - -
707H VAL* 3.3 39.1 + - - +
781H VAL* 1.3 75.7 + - - +
783H PHE* 1.3 61.8 + - - +
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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