Contacts of the strand formed by residues 378 - 380 (chain P) in PDB entry 1IJS
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 TYR 378 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189P ALA 5.5 8.1 - - - -
190P MET* 6.0 2.5 - - - -
376P PRO* 3.6 25.3 - - + +
377P ARG* 1.3 82.1 - - - +
379P ALA* 1.4 54.3 + - - +
380P PHE* 3.7 6.9 - - + -
396P GLU 3.4 0.5 - - - +
397P ARG* 2.3 42.8 - - - +
398P PHE* 3.3 38.6 + + + +
400P TYR* 5.1 0.7 - - + -
463P VAL* 3.2 41.7 - - + +
466P ASN* 3.9 13.2 - - + -
467P GLY* 3.6 28.1 - - - -
468P GLN 4.6 0.4 + - - -
484P VAL 5.5 1.6 + - - -
485P ASN* 4.6 11.4 + - - -
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Residues in contact with ALA 379 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190P MET 5.5 1.7 - - - +
191P ARG* 5.1 1.6 - - - -
192P SER* 3.8 14.9 + - - -
377P ARG* 4.3 2.0 + - + -
378P TYR* 1.4 72.6 - - - +
380P PHE* 1.3 60.7 + - - +
395P PRO* 3.9 22.9 - - + -
396P GLU 3.7 5.2 - - - -
397P ARG* 4.1 11.9 - - - +
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Residues in contact with PHE 380 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192P SER* 3.4 23.1 - - - +
378P TYR* 3.7 9.9 - + + -
379P ALA* 1.3 77.0 - - - +
381P GLY* 1.3 59.4 + - - +
384P HIS* 2.9 28.3 - - + +
385P GLY* 3.9 2.2 - - - -
386P GLN* 3.5 29.6 + - + -
395P PRO* 3.3 25.6 - - - +
396P GLU* 3.4 34.0 + - + -
397P ARG* 4.4 0.2 - - - -
398P PHE* 3.0 37.9 - + - -
466P ASN* 2.4 29.8 - - - +
571P ILE 4.8 4.7 - - - -
572P VAL* 6.4 0.2 - - - -
573P TYR 6.1 0.7 - - - -
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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
------------------------------------------------------------
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