Contacts of the strand formed by residues 731 - 735 (chain T) in PDB entry 2P8Z
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 VAL 731 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730T LEU* 1.3 77.5 - - - +
732T GLU* 1.3 56.9 + - - +
733T ILE* 3.9 25.4 + - + +
747T LEU* 4.8 7.0 - - + -
768T VAL 3.3 3.3 - - - +
769T LYS* 3.3 4.7 - - - -
770T ALA* 2.7 59.1 + - + +
772T LEU* 4.2 22.2 - - + -
780T PHE* 4.3 13.7 - - + -
795T GLN 3.1 17.0 - - - +
796T MET* 3.8 18.6 - - + +
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Residues in contact with GLU 732 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730T LEU* 3.9 3.6 + - + -
731T VAL* 1.3 73.4 - - - +
733T ILE* 1.3 60.9 + - - +
734T GLN* 2.7 35.2 + - - +
767T THR* 4.8 6.9 - - - -
768T VAL 3.6 2.7 - - - +
769T LYS* 3.7 37.7 + - + -
793T PHE 3.6 2.1 - - - +
794T PRO 3.6 1.0 - - - -
795T GLN* 2.8 62.0 + - + +
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Residues in contact with ILE 733 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731T VAL* 3.9 26.0 - - + +
732T GLU* 1.3 79.6 - - - +
734T GLN* 1.3 65.7 + - - +
735T CYS 4.0 0.3 + - - -
743T ILE* 3.5 46.5 - - + +
747T LEU* 5.4 2.9 - - + -
766T PHE 3.6 0.5 - - - +
767T THR* 3.0 5.6 - - - -
768T VAL* 2.8 45.5 + - + +
770T ALA* 6.2 0.7 - - + -
780T PHE* 4.2 10.3 - - + -
784T LEU* 4.1 15.9 - - + -
792T ALA* 3.8 22.2 - - + -
793T PHE 3.5 10.5 - - - +
794T PRO* 4.1 7.2 - - + -
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Residues in contact with GLN 734 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732T GLU* 2.7 36.7 + - - +
733T ILE* 1.3 73.7 - - - +
735T CYS* 1.3 66.3 + - - +
765T LEU* 4.5 16.6 - - + -
766T PHE 3.2 4.3 - - - +
767T THR* 3.4 28.2 - - + +
791T GLN 3.8 1.9 - - - +
792T ALA* 3.7 0.7 - - - -
793T PHE* 3.1 40.0 + - + +
795T GLN* 4.5 7.8 + - - +
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Residues in contact with CYS 735 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733T ILE 4.0 0.8 + - - -
734T GLN* 1.3 76.7 - - - +
736T PRO* 1.3 90.9 - - + +
739T ALA* 3.7 7.2 - - + -
740T VAL* 3.6 27.1 - - - -
743T ILE* 3.9 16.6 - - + -
765T LEU* 3.7 6.3 - - - +
766T PHE* 2.8 36.8 + - - +
768T VAL* 5.8 0.2 - - - -
791T GLN 3.7 13.2 - - - +
792T ALA* 3.7 12.6 - - + -
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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