Contacts of the strand formed by residues 663 - 668 (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 SER 663 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A ASP* 4.4 9.2 + - - -
459A ILE* 5.9 1.0 - - - +
516A LEU* 6.0 0.2 - - - +
517A ALA* 2.9 37.1 + - - +
518A LYS* 4.1 11.8 + - - +
519A MET* 4.1 7.7 - - - +
627A LEU 3.2 9.4 - - - -
628A PHE* 3.9 8.1 - - - -
661A GLN 3.8 4.7 + - - -
662A THR* 1.3 79.3 - - - +
664A LEU* 1.3 66.2 + - - +
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Residues in contact with LEU 664 (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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517A ALA* 3.2 7.4 - - - +
625A TRP 3.8 0.5 - - - +
627A LEU* 2.8 43.1 + - + +
648A TRP* 4.2 37.2 - - + +
649A ARG* 6.1 2.0 - - - +
656A ALA* 5.1 3.8 - - + -
657A ASN 3.6 28.9 - - - +
658A LEU* 4.9 6.5 - - + -
662A THR* 3.8 19.5 - - + -
663A SER* 1.3 82.4 - - - +
665A THR* 1.3 59.2 + - - +
666A LEU* 3.9 18.2 + - + -
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Residues in contact with THR 665 (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 PRO* 4.6 20.8 - - + +
515A CYS 3.3 19.3 - - - +
516A LEU* 3.2 11.8 - - - +
517A ALA 2.7 31.1 + - - +
624A VAL* 3.5 30.1 - - + -
625A TRP 3.4 2.7 - - - -
626A TYR* 3.3 12.8 - - + -
647A LEU 4.5 1.9 - - - +
648A TRP* 3.8 16.8 - - - +
664A LEU* 1.3 71.0 - - - +
666A LEU* 1.3 61.9 + - - +
667A HIS* 4.0 2.5 + - + +
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Residues in contact with LEU 666 (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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623A VAL 4.1 0.2 - - - +
624A VAL* 3.4 3.3 - - - +
625A TRP* 2.7 51.5 + - + +
627A LEU* 3.8 21.1 - - + -
641A PHE* 4.2 13.0 - - + -
646A TYR* 3.6 50.0 - - + +
647A LEU 4.1 3.6 - - - -
648A TRP* 4.2 14.8 - - + -
656A ALA* 3.7 26.9 - - + -
664A LEU* 4.4 16.2 - - + +
665A THR* 1.3 77.6 - - - +
667A HIS* 1.3 58.7 + - - +
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Residues in contact with HIS 667 (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 PRO* 5.7 7.8 - - + +
552A GLN* 5.4 2.2 - - - -
555A VAL* 4.4 7.4 - - + -
622A SER* 3.3 22.5 + - - -
623A VAL 3.3 10.5 - - - -
624A VAL* 3.3 26.7 - - + +
646A TYR* 3.1 1.8 - - - -
647A LEU* 2.6 49.9 + - + +
665A THR* 4.0 1.9 + - + +
666A LEU* 1.3 74.5 - - - +
668A MET* 1.3 69.1 + - - +
669A TRP* 3.3 38.2 - + + -
190D MET* 5.8 11.4 - - + +
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Residues in contact with MET 668 (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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617A MET* 5.8 1.3 - - - -
622A SER 3.7 0.3 - - - -
623A VAL* 2.6 44.9 + - + +
625A TRP* 3.5 33.2 - - + +
641A PHE* 4.2 15.9 - - + -
644A ASN* 3.4 41.5 - - + +
645A THR 3.2 27.6 - - - +
646A TYR* 3.7 9.0 - - + +
667A HIS* 1.3 74.2 - - - +
669A TRP* 1.3 84.4 + - - +
670A PRO* 4.5 6.5 - - - -
694A TYR* 4.2 12.3 - - + +
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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