Contacts of the strand formed by residues 584 - 589 (chain C) in PDB entry 2V4M
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 584 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556C LYS 2.7 20.4 + - - +
557C SER* 3.2 6.7 - - - +
558C VAL 3.1 20.3 + - - -
583C MET* 1.3 66.2 - - - +
585C SER* 1.3 58.1 + - - +
557D SER* 2.5 28.0 + - - +
559D LEU* 3.9 13.9 - - + +
584D HIS* 3.2 52.9 + + - -
586D GLU* 2.8 36.2 + - + +
600D LEU* 3.8 27.6 - - + +
605D MET* 4.7 6.1 - - + -
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Residues in contact with SER 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558C VAL* 3.1 29.2 - - - -
560C ILE* 4.7 1.8 - - - -
574C ALA* 2.6 36.4 + - - +
577C ILE* 3.3 16.7 - - - +
578C LYS* 2.8 48.2 + - - +
583C MET 3.0 4.2 + - - -
584C HIS* 1.3 73.8 - - - +
586C GLU* 1.3 55.1 + - - +
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Residues in contact with GLU 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558C VAL 3.0 6.3 + - - -
559C LEU* 3.5 8.0 - - + +
560C ILE 2.9 23.2 + - - -
574C ALA* 3.6 4.9 - - - -
578C LYS* 4.2 2.0 - - - +
584C HIS 4.0 0.2 + - - -
585C SER* 1.3 75.1 - - - +
587C GLY* 1.3 73.7 + - - +
588C ILE* 3.9 11.3 + - + +
578D LYS* 2.7 40.1 + - - -
584D HIS* 2.7 39.5 + - + +
585D SER 3.9 0.9 - - - +
586D GLU* 3.6 33.6 - - - +
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Residues in contact with GLY 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560C ILE 3.3 9.6 - - - -
567C TYR* 5.2 1.2 + - - -
570C CYS* 3.6 25.6 - - - -
571C LEU* 4.4 17.0 - - - +
574C ALA* 3.3 9.8 - - - +
578C LYS* 5.4 0.2 - - - +
586C GLU* 1.3 82.9 - - - +
588C ILE* 1.3 63.9 + - - +
589C LEU 4.3 0.2 - - - -
586D GLU* 5.2 0.4 + - - -
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Residues in contact with ILE 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559C LEU* 3.9 43.1 - - + -
560C ILE 2.9 9.3 + - - +
561C MET* 3.4 27.8 - - + -
562C GLY 3.4 3.8 + - - +
570C CYS* 3.8 4.9 - - - -
586C GLU* 4.3 17.0 - - + +
587C GLY* 1.3 78.7 - - - +
589C LEU* 1.3 76.5 + - - +
590C ALA 3.2 3.6 + - - -
592C GLU* 5.2 2.2 - - + -
593C LEU* 4.1 21.8 - - + +
597C PRO* 4.3 27.8 - - + +
600C LEU* 5.7 0.4 - - + -
578D LYS* 4.8 4.9 - - - -
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Residues in contact with LEU 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562C GLY 3.4 11.2 - - - +
563C ARG* 3.9 12.3 - - + -
567C TYR* 3.5 50.3 - - + +
588C ILE* 1.3 80.9 - - - +
590C ALA* 1.3 66.3 + - - +
591C GLY 3.2 6.7 - - - +
592C GLU* 2.9 27.0 + - + +
593C LEU 3.6 0.2 + - - -
418D LEU* 3.7 30.5 - - + -
420D SER* 3.8 19.3 - - - +
421D ASP* 3.9 24.9 - - + +
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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