Contacts of the strand formed by residues 584 - 589 (chain B) in PDB entry 1SY7
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 ILE 584 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B GLU* 3.8 21.3 - - - +
292B ASN* 4.2 16.2 - - + +
555B SER* 3.5 35.2 - - - +
556B ARG 2.8 12.4 + - - +
557B ARG* 3.5 8.7 - - + +
558B VAL 2.8 26.5 + - - -
578B ILE* 3.9 3.1 - - - -
582B GLN 4.0 3.6 - - - +
583B ALA* 1.3 79.4 - - - +
585B PRO* 1.3 73.2 - - + +
586B LEU* 3.5 20.9 + - + -
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Residues in contact with PRO 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B VAL 3.5 6.7 - - - +
560B ILE* 4.1 20.9 - - + -
575B TYR* 3.6 37.5 - - + +
578B ILE* 3.8 18.6 - - + -
579B SER* 3.8 11.7 - - - +
583B ALA 3.5 9.9 - - - +
584B ILE* 1.3 88.1 - - + +
586B LEU* 1.3 63.1 + - - +
587B VAL 4.0 0.9 - - - -
606B HIS* 3.5 16.0 + - - -
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Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ARG* 4.0 29.8 - - + -
558B VAL 2.9 12.5 + - - +
559B ALA* 3.2 8.5 - - - -
560B ILE* 2.8 24.9 + - - +
584B ILE* 4.1 17.0 - - + +
585B PRO* 1.3 79.1 - - - +
587B VAL* 1.3 63.4 + - - +
588B ILE* 3.5 12.8 + - + +
606B HIS* 3.6 23.8 - - + +
607B HIS* 5.1 6.1 - - + +
612B PHE* 4.2 17.5 - - + -
617B VAL* 4.1 17.3 - - + -
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Residues in contact with VAL 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B ILE* 3.5 12.3 - - + +
562B ILE* 3.5 32.1 - - + -
571B TYR* 3.4 31.0 - - + +
575B TYR* 3.8 21.8 - - + -
586B LEU* 1.3 71.0 - - - +
588B ILE* 1.3 63.6 + - - +
603B VAL* 4.8 4.5 - - + -
604B GLN 5.0 1.1 - - - +
605B PRO* 3.4 21.7 - - + +
606B HIS* 2.7 41.9 + - + +
607B HIS 3.3 6.9 + - - -
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Residues in contact with ILE 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B ALA* 4.1 10.8 - - + -
560B ILE 2.9 9.6 + - - +
561B ILE* 3.4 10.9 - - + +
562B ILE* 2.9 27.2 + - - +
586B LEU* 3.6 18.4 - - + +
587B VAL* 1.3 80.8 - - - +
589B GLY* 1.3 61.8 + - - +
605B PRO* 4.3 1.3 - - - -
607B HIS* 3.3 29.6 - - + +
608B HIS 4.0 1.8 - - - +
609B LEU* 3.7 36.8 - - + +
612B PHE* 4.4 12.3 - - + -
617B VAL* 6.1 0.2 - - + -
641B TRP* 4.0 30.3 - - + -
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Residues in contact with GLY 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B ILE* 3.4 7.0 - - - -
588B ILE* 1.3 75.3 - - - +
590B PRO* 1.3 67.3 - - - +
591B ARG 3.1 6.3 - - - -
605B PRO* 3.7 17.9 - - - +
607B HIS 3.2 8.1 + - - -
608B HIS* 2.9 8.0 - - - -
609B LEU* 2.8 29.7 + - - -
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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