Contacts of the strand formed by residues 588 - 594 (chain B) in PDB entry 2YA6
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 SER 588 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B TYR* 3.1 5.3 - - - +
576B THR* 3.0 34.0 + - - +
586B SER 2.9 17.7 + - - -
587B GLN* 1.3 70.5 - - - +
589B SER* 1.3 62.1 + - - +
590B ARG* 4.9 3.1 + - - +
606B ALA* 4.4 4.0 - - - -
608B ASN* 2.9 23.2 + - - -
620B SER* 3.6 25.6 - - - -
623B MET* 3.3 9.0 - - - -
630B ASN* 3.0 7.7 + - - -
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Residues in contact with SER 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B VAL 3.5 7.0 - - - -
588B SER* 1.3 73.9 - - - +
590B ARG* 1.3 65.6 + - - +
606B ALA* 3.5 2.6 - - - +
607B VAL* 3.2 24.1 + - - +
630B ASN* 2.8 30.6 + - - +
631B THR 2.7 23.6 + - - -
633B SER* 4.1 5.4 - - - -
645B LEU* 3.9 19.7 - - - -
647B MET* 3.5 13.8 - - - +
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Residues in contact with ARG 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B TRP* 3.4 19.6 - - - -
548B MET* 3.7 18.8 - - - +
551B LEU* 5.6 1.1 - - - -
573B PRO* 3.7 2.3 - - - +
574B VAL* 2.9 47.6 + - + +
575B TYR* 5.2 0.9 - - - -
576B THR* 4.1 14.4 + - + +
588B SER 4.9 1.7 + - - +
589B SER* 1.3 78.0 - - - +
591B VAL* 1.3 74.1 + - - +
592B ILE* 5.6 0.7 - - - -
603B ALA* 4.5 11.9 - - - +
604B GLY 2.8 32.8 + - - +
605B GLU* 3.4 19.5 - - - +
606B ALA* 3.7 18.7 - - - +
609B ASP* 4.0 4.9 + - - -
620B SER* 2.9 29.1 + - - -
633B SER* 4.7 0.3 + - - -
645B LEU* 4.5 9.7 - - - +
666B TRP* 4.7 3.4 - - - +
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Residues in contact with VAL 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B LEU* 4.0 31.2 - - + -
572B ILE 3.3 15.7 - - - +
573B PRO* 3.9 11.2 - - + -
574B VAL* 4.1 2.7 - - - -
590B ARG* 1.3 83.6 - - - +
592B ILE* 1.3 63.8 + - - +
593B TYR* 4.8 3.4 - - + -
603B ALA* 3.8 1.2 - - - -
604B GLY* 2.8 31.7 + - - -
605B GLU 4.7 2.0 + - - -
635B VAL* 4.6 7.6 - - + -
645B LEU* 4.3 18.2 - - + -
663B GLY* 3.3 30.5 + - - +
666B TRP* 4.6 6.6 - - + -
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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
----------------------------------------------------------
417B ILE* 4.6 2.7 - - + -
521B LEU* 4.0 13.0 - - + -
539B ILE* 3.9 27.4 - - + -
543B VAL* 3.7 30.3 - - + -
551B LEU* 5.1 3.8 - - + -
571B LEU* 3.7 1.6 - - - -
572B ILE* 3.0 55.9 + - + +
574B VAL* 4.0 19.7 - - + +
590B ARG* 5.6 0.4 - - - -
591B VAL* 1.3 78.4 - - - +
593B TYR* 1.3 63.6 + - - +
601B TRP* 4.1 14.1 - - + -
602B HIS 3.0 9.9 - - - +
603B ALA* 4.2 7.4 - - + -
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Residues in contact with TYR 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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569B ARG* 3.3 28.5 + - + -
570B ILE 3.0 14.4 - - - +
571B LEU* 3.6 15.5 - - + -
591B VAL* 4.6 6.3 - - + -
592B ILE* 1.3 78.2 - - - +
594B SER* 1.3 61.7 + - - +
595B ASP* 3.7 20.4 - - - -
600B THR 4.0 0.2 - - - +
601B TRP* 3.4 8.8 - - - -
602B HIS* 2.8 69.7 + + + +
603B ALA 4.0 4.5 + - - -
604B GLY* 3.8 19.1 - - - -
662B GLY 5.5 0.4 - - - -
663B GLY 5.3 0.7 - - - -
664B VAL* 3.8 31.2 - - + +
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Residues in contact with SER 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B GLY 4.1 1.9 - - - +
569B ARG* 3.4 4.0 - - - -
570B ILE* 3.0 34.3 + - - +
593B TYR* 1.3 75.5 - - - +
595B ASP* 1.3 62.1 + - - +
596B ASP* 2.7 27.5 + - - -
597B HIS 4.8 0.8 + - - -
598B GLY* 2.8 24.5 + - - -
600B THR 2.8 14.6 + - - -
601B TRP* 3.7 20.5 - - - -
602B HIS* 5.2 0.9 - - - -
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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