Contacts of the strand formed by residues 623 - 628 (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 VAL 623 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557A LYS* 4.0 8.7 - - + +
559A PHE* 3.7 27.1 - - + -
617A MET* 3.6 26.7 - - + -
621A ASP* 4.0 10.5 - - + +
622A SER* 1.3 70.5 - - - +
624A VAL* 1.3 60.4 + - - +
625A TRP* 3.2 30.6 + - + +
667A HIS* 3.3 1.9 - - - -
668A MET* 2.6 50.5 + - + +
670A PRO* 3.7 21.5 - - + -
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Residues in contact with VAL 624 (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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552A GLN* 3.8 7.9 - - - +
555A VAL* 3.5 30.7 - - + -
557A LYS 3.5 7.6 + - - +
558A GLU* 4.0 0.3 - - - -
559A PHE 3.5 10.5 + - - -
622A SER 3.7 0.4 - - - +
623A VAL* 1.3 72.1 - - - +
625A TRP* 1.3 57.6 + - - +
626A TYR* 3.2 41.1 - - + +
665A THR* 3.5 31.0 - - + -
666A LEU 3.5 4.5 - - - +
667A HIS* 3.3 37.9 - - + +
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Residues in contact with TRP 625 (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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559A PHE* 3.4 47.1 - + + -
561A LEU* 3.4 38.1 - - + -
615A LEU* 3.7 16.8 - - + -
617A MET* 4.3 8.7 - - + -
623A VAL* 3.2 24.9 - - + +
624A VAL* 1.3 71.1 - - - +
626A TYR* 1.3 60.9 + - - +
627A LEU* 3.9 6.7 - - + -
641A PHE* 3.4 31.2 - + - -
646A TYR* 5.5 1.1 - - + -
664A LEU 3.8 0.5 - - - +
665A THR* 3.4 3.1 - - - +
666A LEU* 2.7 61.2 + - + +
668A MET* 3.5 32.4 - - + +
678A VAL* 5.0 0.9 - - + -
694A TYR* 4.3 16.2 - + + -
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Residues in contact with TYR 626 (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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515A CYS* 3.6 23.1 - - + -
516A LEU 4.4 1.8 - - - -
517A ALA* 3.8 17.5 - - + -
539A LYS* 3.8 11.1 - - + -
552A GLN* 2.7 26.3 + - - -
558A GLU* 3.5 27.0 + - + +
559A PHE 2.8 27.3 + - - +
560A TYR* 3.4 42.5 - + + +
561A LEU 3.3 22.0 + - - +
624A VAL* 3.2 18.7 - - + +
625A TRP* 1.3 70.9 - - - +
627A LEU* 1.3 62.6 + - - +
628A PHE* 4.4 4.2 - - + -
664A LEU 3.6 3.6 - - - -
665A THR* 3.3 34.1 - - + -
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Residues in contact with LEU 627 (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* 3.4 5.0 - - - +
561A LEU* 3.4 44.9 - - + +
563A PRO* 5.2 0.9 - - + -
625A TRP* 4.6 10.8 - - + -
626A TYR* 1.3 77.5 - - - +
628A PHE* 1.3 66.9 + - - +
639A ILE* 4.4 15.0 - - + -
641A PHE* 5.0 2.2 - - + -
656A ALA* 3.9 16.6 - - + -
658A LEU* 4.1 24.9 - - + -
663A SER* 3.2 1.6 - - - -
664A LEU* 2.8 39.0 + - + +
666A LEU* 3.8 30.7 - - + -
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Residues in contact with PHE 628 (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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430A LEU* 3.6 27.4 - - + -
517A ALA* 5.2 2.5 - - + -
518A LYS 4.0 10.3 - - - -
519A MET* 3.5 31.2 - - + -
535A ILE* 3.8 17.0 - - + -
537A PRO* 3.7 33.4 - - + -
560A TYR* 4.8 5.8 - + + -
561A LEU 3.3 6.2 + - - -
562A PHE* 3.3 52.3 - + + -
563A PRO* 3.4 7.3 - - - +
626A TYR* 4.4 8.7 - - + -
627A LEU* 1.3 80.3 - - - +
629A SER* 1.3 62.6 + - - +
658A LEU* 3.7 5.4 - - - -
662A THR 3.0 15.3 - - - +
663A SER* 3.9 5.6 - - - -
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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