Contacts of the strand formed by residues 624 - 628 (chain B) in PDB entry 5IJ7
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 TRP 624 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL* 3.7 22.7 - - + -
108B PRO* 3.0 38.8 + - + -
109B ILE 3.4 19.0 + - - -
110B MET* 3.6 22.6 - - + +
616B LEU* 3.6 23.3 - - + -
617B ALA 3.6 19.5 - - - -
618B PRO* 3.7 18.8 - - + -
619B SER* 3.8 2.0 - - - -
623B GLY* 1.3 75.0 - - - -
625B GLY* 1.3 53.7 + - - +
686B PHE* 3.7 19.1 - - + +
688B ASN* 2.8 25.2 + - - +
9001B 6BN 2.8 31.3 + - - +
566T PHE* 3.9 28.0 - + + -
571T CYS* 3.9 22.9 - - + -
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Residues in contact with GLY 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B LEU* 3.5 9.7 - - - +
617B ALA 2.9 33.9 + - - +
619B SER* 3.6 4.1 - - - +
624B TRP* 1.3 74.9 - - - +
626B ILE* 1.3 61.0 + - - -
627B PHE* 3.8 3.8 - - - -
686B PHE* 3.2 12.1 - - - -
688B ASN* 3.5 8.5 - - - -
721B GLU* 3.9 10.5 - - - -
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Residues in contact with ILE 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B LEU* 3.7 20.4 - - + -
615B LEU 3.4 21.5 - - - +
616B LEU* 4.1 6.5 - - + +
625B GLY* 1.3 72.4 - - - -
627B PHE* 1.3 61.2 + - - +
683B LYS* 3.5 41.5 - - + +
684B ILE* 4.3 6.1 - - + -
686B PHE* 3.3 18.3 + - + -
687B ALA* 3.6 33.6 - - + +
688B ASN* 4.9 0.2 - - - +
721B GLU* 3.4 5.9 - - - +
722B LEU* 2.8 49.8 + - + -
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Residues in contact with PHE 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B LEU* 3.5 4.4 - - - -
615B LEU* 2.8 46.0 + - + +
617B ALA* 3.4 38.1 - - + -
618B PRO 3.7 10.8 - - - -
619B SER* 4.4 0.2 - - - -
625B GLY 3.8 8.5 - - - -
626B ILE* 1.3 74.9 - - - +
628B ILE* 1.3 63.3 + - - +
719B GLY 3.4 23.1 - - - +
720B GLU 3.4 5.6 - - - +
721B GLU* 3.4 43.1 - - + -
563T ARG* 3.3 37.2 - - - -
565T TYR* 3.8 22.9 - + + +
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Residues in contact with ILE 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B LYS* 4.3 11.0 - - + -
613B HIS 4.0 6.5 - - - +
614B LEU* 3.9 12.1 - - + -
615B LEU* 4.9 1.5 - - - +
627B PHE* 1.3 71.6 - - - +
629B LYS* 1.3 60.4 + - - +
630B ASP 3.5 19.7 - - - +
632B VAL* 4.1 19.1 - - + -
638B ILE* 3.8 39.7 - - + -
716B ILE* 3.7 17.3 - - + +
717B GLN 3.4 22.4 - - - +
719B GLY* 2.9 30.0 + - - -
720B GLU 3.2 10.2 + - - +
722B LEU* 4.3 14.7 - - + +
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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
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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