Contacts of the strand formed by residues 594 - 600 (chain B) in PDB entry 1M2V
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 TYR 594 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B VAL* 3.4 5.2 - - - +
207B ILE* 2.8 39.0 + - + +
209B PRO* 3.9 33.7 - - + -
558B MET* 4.6 8.5 - - - -
572B TYR 3.6 7.9 - - - +
573B GLY* 4.0 4.5 - - - -
574B HIS 3.8 23.8 + - - -
575B PHE* 3.9 22.4 - + + -
585B PHE* 3.7 17.9 - + - -
588B MET* 4.5 5.8 - - + +
589B PRO* 3.7 23.7 + - - +
592B GLN* 3.6 35.2 + - + +
593B SER* 1.3 87.0 + - - +
595B LEU* 1.3 62.0 + - - +
596B PHE* 4.6 9.0 - - + -
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Residues in contact with LEU 595 (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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185B THR* 5.3 0.4 - - + -
204B GLY 4.6 0.9 - - - -
205B LEU 3.2 18.8 - - - +
206B VAL* 3.8 23.1 - - + -
571B PHE* 3.6 0.3 - - - -
572B TYR* 2.7 70.4 + - + +
594B TYR* 1.3 77.4 - - - +
596B PHE* 1.3 70.2 + - - +
650B ALA 4.8 0.4 - - - +
653B SER* 4.6 4.7 - - - +
654B PHE* 3.8 48.9 - - + +
657B SER* 4.0 23.3 - - - +
658B LYS* 5.8 0.2 - - + -
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Residues in contact with PHE 596 (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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204B GLY* 3.1 4.0 - - - -
205B LEU* 2.8 38.5 + - + +
207B ILE* 3.4 30.1 - - + -
558B MET* 4.1 21.5 - - + -
559B ARG* 4.9 0.7 - - - -
560B ALA* 3.6 20.9 - - + -
568B MET* 3.3 33.7 - - + -
570B ARG 3.4 4.7 - - - +
571B PHE* 3.3 37.5 - + + -
575B PHE* 4.6 3.6 - + - -
583B CYS* 3.8 19.3 - - - -
594B TYR* 4.6 12.6 - - + -
595B LEU* 1.3 86.1 - - - +
597B GLU* 1.3 61.6 + - - +
598B VAL* 3.7 1.9 + - - +
613B VAL* 5.3 0.4 - - + -
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Residues in contact with GLU 597 (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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203B PHE 3.6 6.5 - - - +
568B MET* 3.8 2.9 - - - +
569B SER* 3.0 35.7 + - - +
570B ARG* 2.9 56.7 + - + +
572B TYR* 4.7 5.8 - - + -
595B LEU* 4.2 2.0 - - - +
596B PHE* 1.3 73.9 - - - +
598B VAL* 1.3 67.9 + - - +
599B ASN* 5.0 5.6 - - - +
654B PHE* 3.3 33.6 - - + -
658B LYS* 3.0 15.2 + - - -
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Residues in contact with VAL 598 (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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196B LEU* 4.9 1.9 - - - +
203B PHE* 2.8 63.2 + - + +
204B GLY* 4.5 1.3 - - - -
205B LEU* 3.8 34.3 - - + -
566B LEU* 4.3 10.1 - - + -
567B ARG 3.4 24.7 - - - +
568B MET* 3.8 16.8 - - - -
596B PHE 3.8 2.9 - - - +
597B GLU* 1.3 81.9 - - - +
599B ASN* 1.3 71.1 + - - +
611B VAL* 5.3 1.6 - - + -
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Residues in contact with ASN 599 (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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196B LEU* 5.1 4.1 - - - +
565B GLY 3.5 0.7 - - - +
566B LEU* 3.6 1.4 - - - -
567B ARG* 2.8 73.1 + - - +
569B SER* 3.2 23.0 + - - -
597B GLU* 5.0 6.3 - - - +
598B VAL* 1.3 78.0 - - - +
600B VAL* 1.3 62.1 + - - +
601B ASP* 3.2 8.9 + - - +
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Residues in contact with VAL 600 (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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189B VAL* 4.0 8.5 - - + -
190B PRO* 3.8 11.0 - - + +
192B ASN* 4.3 13.2 - - - -
193B SER* 3.4 15.4 + - - +
196B LEU* 3.7 25.3 - - + +
203B PHE* 3.4 37.2 - - + -
565B GLY 3.4 3.6 - - - +
566B LEU* 3.9 4.9 - - + -
599B ASN* 1.3 71.0 - - - +
601B ASP* 1.3 70.4 + - - +
602B GLU 3.2 1.0 + - - -
603B SER* 5.2 0.9 - - - -
604B ILE* 3.4 34.5 - - + +
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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