Contacts of the strand formed by residues 703 - 707 (chain K) in PDB entry 6PA7
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 703 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634K ILE* 5.3 5.4 - - + -
635K ARG 3.0 3.3 + - - +
636K VAL* 3.2 26.5 - - + +
637K LEU 2.9 26.9 + - - +
650K LEU* 4.4 9.9 - - + -
701K PHE* 3.7 0.8 - - - +
702K ASP* 1.3 80.3 - - + +
704K VAL* 1.3 65.5 + - - +
705K ILE* 4.0 16.8 - - + -
752K PHE* 3.4 29.4 - - + +
753K TRP* 4.5 2.9 - - - +
754K LEU* 5.4 0.7 - - + -
798K LEU* 4.8 3.8 - - + -
902K PHE* 3.7 33.4 - - + -
905K LEU* 3.9 23.8 - - + -
909K PHE* 6.3 1.6 - - + -
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Residues in contact with VAL 704 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637K LEU* 3.3 15.3 - - + +
639K LEU* 3.8 26.0 - - + -
701K PHE* 4.4 3.6 - - + -
703K LEU* 1.3 76.5 - - - +
705K ILE* 1.3 66.9 + - - +
734K PHE* 3.8 16.4 - - + -
737K LEU 5.3 1.1 - - - +
738K LEU* 4.8 12.1 - - + -
741K ALA* 4.0 14.8 - - + -
751K PHE* 3.6 29.4 - - + -
752K PHE 3.0 10.3 + - - +
753K TRP* 3.1 8.4 - - + -
754K LEU 2.9 26.0 + - - -
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Residues in contact with ILE 705 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636K VAL* 4.4 12.1 - - + -
637K LEU 2.9 17.4 + - - +
638K SER* 3.6 24.5 - - - +
639K LEU* 3.0 30.8 + - - +
641K ASP* 5.4 0.2 - - - +
646K GLY* 4.1 19.3 - - - +
660K TYR* 4.6 2.0 - - + +
703K LEU* 4.0 12.3 - - + -
704K VAL* 1.3 80.1 - - - +
706K GLY* 1.3 59.4 + - - +
734K PHE* 4.0 4.7 - - - -
754K LEU* 3.3 19.3 - - + +
893K TRP* 3.7 25.4 - - + -
902K PHE* 3.6 27.8 - - + -
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Residues in contact with GLY 706 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638K SER* 5.7 0.2 - - - -
639K LEU* 4.7 0.4 - - - -
640K PHE* 4.3 16.2 - - - -
705K ILE* 1.3 78.4 - - - +
707K GLY* 1.3 58.5 + - - -
734K PHE* 4.2 7.8 - - - -
754K LEU 3.1 6.3 + - - +
755K PHE* 3.3 13.8 - - - -
756K GLU 3.0 22.2 + - - -
893K TRP* 3.5 15.3 - - - -
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Residues in contact with GLY 707 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640K PHE* 3.2 25.1 + - - +
706K GLY* 1.3 74.3 - - - -
708K SER* 1.3 67.9 + - - +
755K PHE* 4.1 0.4 - - - -
756K GLU* 3.4 28.7 - - - -
893K TRP* 3.7 4.8 - - - +
1001K SAH 3.4 18.6 - - - +
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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