Contacts of the strand formed by residues 757 - 761 (chain B) 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 757 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B GLY* 4.1 0.2 - - - -
534B ILE* 2.7 50.3 + - + +
666B LEU* 5.1 16.6 - - + +
756B VAL* 1.3 70.9 - - - +
758B ALA* 1.3 67.3 + - + +
786C GLU* 6.2 2.5 - - - -
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Residues in contact with ALA 758 (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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533B GLY* 3.5 11.1 - - - -
534B ILE* 4.0 22.8 - - + +
694B ASN* 5.4 2.5 - - + -
756B VAL 3.8 0.4 + - - -
757B PHE* 1.3 79.5 - - + +
759B SER* 1.3 65.6 + - - +
760B THR* 3.2 7.4 + - - -
780C HIS* 3.3 25.6 - - - +
781C GLU* 4.7 8.1 - - - +
782C ASN 4.6 6.8 + - - +
786C GLU* 5.8 5.3 - - - +
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Residues in contact with SER 759 (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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532B THR 4.0 5.2 - - - -
533B GLY* 5.0 0.7 - - - -
756B VAL* 4.2 12.9 + - - -
757B PHE 3.6 0.6 - - - -
758B ALA* 1.3 70.9 - - - +
760B THR* 1.3 57.9 + - - +
535C TYR* 3.7 15.3 + - - -
780C HIS* 2.6 54.1 + - - +
785C MET* 5.9 2.2 - - - +
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Residues in contact with THR 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B THR* 4.4 13.5 - - - -
515B ILE* 3.8 21.8 - - - -
531B GLU* 3.7 3.5 - - - +
532B THR 2.8 28.0 + - - +
533B GLY* 4.8 2.7 - - - -
758B ALA 3.2 7.6 + - - -
759B SER* 1.3 75.8 - - - +
761B GLY* 1.3 60.6 + - - +
535C TYR* 3.5 25.6 - - - -
780C HIS* 5.4 3.4 - - - -
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Residues in contact with GLY 761 (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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514B THR* 4.8 0.4 - - - -
515B ILE* 3.2 30.0 + - - +
528B PRO* 4.3 10.8 - - - -
530B ILE 3.2 13.2 - - - -
531B GLU* 4.1 1.6 - - - -
532B THR* 3.6 10.5 - - - +
760B THR* 1.3 83.1 - - - +
762B TYR* 1.3 68.3 + - - -
535C TYR* 3.8 2.8 + - - -
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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