Contacts of the strand formed by residues 591 - 596 (chain B) in PDB entry 5M5X
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 LYS 591 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B HIS* 4.5 0.4 - - - -
362B LEU* 3.7 28.7 - - + +
369B ASP* 6.0 4.7 - - + +
373B MET* 5.1 1.8 - - - -
558B VAL* 4.9 15.5 - - + -
562B PRO* 3.0 23.5 - - - +
587B GLN* 4.2 1.0 - - - -
588B ILE* 2.8 69.0 + - + +
589B ASP* 3.1 7.7 + - - +
590B GLY* 1.3 75.8 - - - +
592B ILE* 1.3 66.6 + - - +
593B ILE* 3.1 19.6 - - + +
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Residues in contact with ILE 592 (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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369B ASP* 5.2 12.1 + - + +
372B ARG* 5.3 12.8 - - + -
373B MET* 3.6 46.9 - - + +
376B PHE* 5.8 3.6 - - + -
573B ALA* 3.7 16.8 - - + +
586B VAL 4.4 0.4 - - - -
587B GLN* 3.2 35.0 - - + +
590B GLY 3.7 2.7 - - - +
591B LYS* 1.3 86.2 - - - +
593B ILE* 1.3 65.8 + - - +
594B GLY* 3.5 18.4 - - - +
595B TRP* 4.1 19.7 - - + -
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Residues in contact with ILE 593 (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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562B PRO* 3.9 17.7 - - + +
565B LEU* 4.3 11.4 - - + -
566B TYR* 5.5 11.0 - - + -
570B VAL* 4.0 25.1 - - + -
571B ALA 3.6 4.8 - - - +
572B PRO* 4.2 1.1 - - + +
573B ALA* 3.1 25.9 + - - +
586B VAL* 3.4 20.2 + - + +
587B GLN* 4.9 0.2 - - - +
588B ILE* 3.7 27.4 - - + -
591B LYS* 3.1 28.4 + - + +
592B ILE* 1.3 75.6 - - - +
594B GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 594 (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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570B VAL* 4.7 4.9 - - - -
571B ALA 4.2 5.2 - - - -
572B PRO 4.7 0.4 - - - -
573B ALA* 4.3 6.3 - - - -
585B CYS* 4.0 0.3 - - - -
586B VAL* 3.2 26.8 + - - +
587B GLN* 4.3 0.7 - - - +
592B ILE* 3.5 8.3 - - - +
593B ILE* 1.3 82.9 - - - +
595B TRP* 1.3 83.6 + - - -
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Residues in contact with TRP 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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372B ARG* 5.5 10.3 - - + -
376B PHE* 3.4 46.5 - + + -
570B VAL* 4.6 2.5 - - - -
571B ALA* 3.5 25.5 + - - +
573B ALA* 5.1 2.9 - - + -
576B THR* 3.3 50.1 + - + +
578B ALA 3.7 17.3 - - - +
579B ALA* 4.6 5.0 - - + +
580B GLY 5.3 0.9 - - - -
583B LEU* 3.8 26.6 - - + +
584B CYS 3.2 24.0 - - - +
585B CYS* 2.9 35.1 - - + +
586B VAL* 5.7 0.2 - - - -
587B GLN* 4.6 1.8 - - - -
592B ILE* 4.1 16.6 - - + -
594B GLY* 1.3 83.3 - - - -
596B VAL* 1.3 59.9 + - - +
637B TYR* 4.6 2.4 + - - -
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Residues in contact with VAL 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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568B LEU* 5.8 0.2 - - + -
569B GLY 3.7 20.0 - - - +
570B VAL* 3.9 29.6 - - + +
571B ALA* 4.0 6.1 - - + +
583B LEU* 3.3 11.8 - - - +
584B CYS* 3.0 40.6 + - - -
586B VAL* 5.2 1.3 - - + +
595B TRP* 1.3 74.3 - - - +
597B SER* 1.3 76.6 + - - +
600B GLN* 3.3 26.0 - - + +
601B GLY* 5.4 1.1 - - - +
138N SER* 5.7 2.0 - - - +
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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