Contacts of the strand formed by residues 558 - 561 (chain A) in PDB entry 4EJX
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 GLU 558 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A GLU* 6.1 0.5 - - - +
426A HIS* 3.9 14.0 - - - -
539A LYS* 2.7 36.5 + - - -
551A ARG* 3.6 20.4 - - + +
552A GLN* 2.9 38.5 + - - +
555A VAL* 4.1 9.0 - - + -
557A LYS* 1.3 79.9 - - - +
559A PHE* 1.3 65.7 + - - +
560A TYR* 4.0 14.6 + - + -
624A VAL 4.0 4.0 - - - +
626A TYR* 3.5 17.4 + - + +
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Residues in contact with PHE 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU 5.9 0.2 - - - -
426A HIS* 3.8 12.6 - + - -
557A LYS* 4.0 16.2 - - + -
558A GLU* 1.3 79.1 - - - +
560A TYR* 1.3 59.7 + - - +
561A LEU 4.1 0.7 - - - -
614A GLY 3.3 22.9 - - - -
615A LEU* 3.6 33.9 - - + -
616A THR 3.7 17.3 - - - -
617A MET* 3.6 21.3 - - + -
623A VAL* 3.7 26.9 - - + -
624A VAL 3.5 6.7 + - - -
625A TRP* 3.4 34.8 - + + -
626A TYR* 2.8 37.1 + - - -
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Residues in contact with TYR 560 (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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426A HIS* 3.0 28.8 + + - +
427A LEU* 3.9 11.0 - - + -
430A LEU* 4.0 13.2 - - + +
433A VAL* 3.3 43.0 - - + +
537A PRO* 3.8 16.4 - - + -
538A MET 4.4 5.4 - - - -
539A LYS* 3.3 36.2 + - + +
558A GLU* 4.0 21.1 + - + -
559A PHE* 1.3 72.8 - - - +
561A LEU* 1.3 62.5 + - - +
605A ASN* 3.1 19.4 + - - +
626A TYR* 3.4 40.8 - + + +
628A PHE* 4.8 4.5 - + + -
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Residues in contact with LEU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A HIS* 4.9 0.4 - - + -
559A PHE 4.1 0.2 - - - -
560A TYR* 1.3 75.5 - - - +
562A PHE* 1.3 60.2 + - - +
563A PRO* 3.3 13.1 - - + +
604A MET* 4.3 8.5 - - + -
605A ASN* 3.4 8.3 - - - +
612A GLN* 3.4 33.0 - - - +
615A LEU* 3.8 17.5 - - + -
625A TRP* 3.4 32.1 - - + -
626A TYR 3.3 6.9 + - - +
627A LEU* 3.4 19.2 - - + +
628A PHE* 3.3 21.3 + - - -
639A ILE* 4.7 3.4 - - + -
641A PHE* 3.8 6.7 - - + -
678A VAL* 3.5 27.6 - - + -
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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