Contacts of the strand formed by residues 758 - 762 (chain A) in PDB entry 4PE5
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 758 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A PHE* 3.5 28.9 - + - -
516A PRO* 3.8 12.8 - - + -
517A LEU 3.3 7.0 - - - +
518A THR* 3.4 31.9 - - + -
519A ILE* 4.1 2.5 - - - -
532A PRO* 3.2 3.8 - - - +
533A PHE* 3.0 45.7 + + + -
534A LYS* 3.2 28.2 + - + +
536A GLN* 3.9 12.8 - - + -
732A ASP* 3.4 33.0 - - + -
734A ALA* 3.8 13.2 - - + -
735A VAL* 5.5 1.1 - - + -
756A SER* 5.6 1.1 - - - -
757A GLY* 1.3 81.0 - - - -
759A GLY* 1.3 58.5 + - - +
942A GLY 3.6 7.9 - - - -
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Residues in contact with GLY 759 (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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513A ILE 4.1 1.2 - - - +
515A ALA 3.8 3.5 - - - +
517A LEU* 3.0 30.0 + - - +
519A ILE* 3.7 19.7 - - - +
529A PHE* 4.9 3.8 - - - -
530A SER* 4.3 7.4 - - - -
531A LYS 4.8 0.9 - - - -
533A PHE* 3.6 15.3 - - - -
758A PHE* 1.3 75.6 - - - +
760A ILE* 1.3 64.1 + - - -
761A GLY 3.6 0.5 + - - -
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Residues in contact with ILE 760 (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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462A LEU* 4.5 5.2 - - + -
466A LEU* 4.4 9.9 - - + -
512A MET* 3.6 34.3 - - + -
513A ILE 3.6 7.0 - - - +
514A VAL* 5.0 9.6 - - + -
529A PHE* 3.7 11.3 - - - -
530A SER* 3.2 34.4 + - - +
531A LYS 4.9 0.2 - - - +
533A PHE* 3.6 26.9 - - + -
759A GLY* 1.3 71.2 - - - -
761A GLY* 1.3 67.0 + - - +
762A MET* 3.5 12.7 + - + +
772A VAL* 3.7 24.5 - - + -
776A ILE* 3.9 19.1 - - + -
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Residues in contact with GLY 761 (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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505A LEU* 4.2 5.2 - - - -
512A MET* 3.4 7.8 - - - +
513A ILE* 2.9 51.4 + - - +
517A LEU* 4.1 2.0 - - - +
527A ILE* 4.6 0.2 - - - -
529A PHE* 4.1 15.0 - - - -
759A GLY 3.6 2.6 + - - -
760A ILE* 1.3 70.9 - - - +
762A MET* 1.3 70.3 + - - +
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Residues in contact with MET 762 (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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505A LEU* 4.0 5.6 - - - +
511A ASP 4.9 4.9 - - - +
512A MET* 3.7 26.7 - - + -
527A ILE* 3.2 5.8 - - - +
528A GLU* 2.8 47.2 + - + +
529A PHE* 5.3 1.8 - - - -
530A SER* 5.4 1.3 - - - +
760A ILE* 3.7 17.0 - - + +
761A GLY* 1.3 82.7 - - - +
763A ARG* 1.3 62.3 + - - +
764A LYS 3.2 2.3 + - - +
766A SER* 3.8 18.6 - - - +
768A TRP* 3.5 17.3 - - + +
769A LYS* 3.5 47.6 - - + +
772A VAL* 5.0 0.4 - - + -
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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