Contacts of the strand formed by residues 637 - 641 (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 HIS 637 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A PRO* 3.2 25.5 + - + -
564A THR* 3.6 8.7 - - - -
565A VAL 4.6 0.2 - - - -
629A SER* 3.3 25.5 + - - -
635A ASP* 3.5 29.7 - - + +
636A VAL* 1.3 78.0 - - - +
638A GLY* 1.3 58.2 + - - +
639A ILE* 3.8 13.7 - - + +
657A ASN* 3.1 28.2 - - - +
658A LEU* 3.1 30.3 + - + +
659A PHE* 5.5 0.5 - - - -
680A CYS* 3.9 0.2 - - - -
682A THR* 3.7 3.6 - - - -
685A HIS* 3.7 11.9 - + - -
690A MET* 3.5 12.1 - - - -
1000A PHE* 5.2 0.5 - - - +
1001A PRO* 4.7 1.7 - - - +
1105A CU 2.8 22.2 - - - -
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Residues in contact with GLY 638 (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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637A HIS* 1.3 74.0 - - - +
639A ILE* 1.3 63.7 + - - +
640A TYR 3.2 1.6 + - - -
655A THR* 3.5 8.2 - - - +
656A ALA 3.3 6.7 - - - -
657A ASN* 4.1 1.6 - - - -
680A CYS* 3.7 2.4 - - - -
681A LEU* 2.6 34.3 + - - +
682A THR* 3.6 8.5 + - - -
1001A PRO 3.6 20.6 - - - -
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Residues in contact with ILE 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A LEU* 4.7 2.7 - - + -
563A PRO* 3.4 38.1 - - + -
604A MET* 3.8 20.0 - - + -
627A LEU* 4.4 17.3 - - + -
637A HIS* 3.8 9.9 - - + -
638A GLY* 1.3 68.3 - - - -
640A TYR* 1.3 60.4 + - - +
641A PHE* 4.3 9.7 - - + -
654A ASP 3.6 2.9 - - - +
655A THR* 3.4 1.4 - - - -
656A ALA* 2.8 41.1 + - - +
658A LEU* 4.1 13.9 - - + -
678A VAL* 3.9 17.0 - - + +
679A GLU 4.1 2.9 - - - +
680A CYS* 3.7 28.3 - - + -
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Residues in contact with TYR 640 (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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638A GLY 4.1 1.6 - - - +
639A ILE* 1.3 73.3 - - - +
641A PHE* 1.3 75.5 + - - +
642A SER* 3.7 25.5 - - - -
643A GLY 4.2 3.1 + - - -
654A ASP* 2.9 35.7 - - - -
655A THR* 3.8 13.5 - - + -
677A ASN 3.1 14.4 - - - +
678A VAL* 3.6 2.6 - - - -
679A GLU* 2.9 58.0 + - + +
681A LEU* 4.3 9.9 - - + -
816A HIS* 4.0 4.2 + - - -
817A ALA 3.6 15.2 + - - -
818A HIS* 3.3 28.3 - + - -
819A GLY 4.3 1.1 + - - -
861A TYR* 3.4 28.7 + + - -
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Residues in contact with PHE 641 (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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561A LEU* 3.8 11.4 - - + -
625A TRP* 3.4 58.1 - + + -
627A LEU* 5.0 2.7 - - + -
639A ILE* 4.3 14.6 - - + -
640A TYR* 1.3 85.2 - - - +
642A SER* 1.3 64.7 + - - +
643A GLY 3.6 0.3 + - - -
644A ASN 3.2 20.3 - - - +
646A TYR* 4.5 10.1 - + + -
654A ASP* 3.1 21.2 + - - +
666A LEU* 4.2 21.5 - - + -
668A MET* 4.2 11.9 - - + -
677A ASN 3.6 1.8 - - - -
678A VAL* 3.9 14.6 - - + -
694A TYR* 3.3 33.2 - + - +
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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