Contacts of the strand formed by residues 574 - 580 (chain B) in PDB entry 2H3W
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 574 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441B TYR* 4.7 4.5 - + - -
444B ILE* 5.4 1.6 - - - +
445B TYR* 2.7 31.9 + + - -
549B PHE 5.0 0.2 - - - +
550B ASN* 2.7 16.1 + - + +
551B LEU* 4.1 13.6 - - + +
552B SER* 3.1 29.3 + - - +
568B PRO* 3.8 5.6 - - - +
569B VAL 5.0 0.4 + - - +
572B ASP 5.4 0.7 - - - -
573B GLY* 1.3 77.0 - - - -
575B GLY* 1.3 60.3 - - - +
576B ILE* 3.9 10.2 + - + +
589B VAL* 3.9 13.0 - - + -
590B SER 3.2 15.5 - - - +
591B ALA* 3.8 4.7 - - + -
598B THR* 3.6 13.5 - - + -
599B ASN* 2.9 41.0 + - - +
600B ALA 3.9 0.7 - - - -
602B ARG* 5.6 0.9 - - - +
603B MET* 3.2 48.8 + - + +
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Residues in contact with GLY 575 (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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552B SER* 3.5 5.8 - - - -
566B PHE* 3.6 22.3 - - - +
568B PRO* 3.6 7.6 - - - +
574B TYR* 1.3 73.2 - - - +
576B ILE* 1.3 59.9 + - - -
577B CYS 4.2 0.4 + - - -
588B SER* 3.4 6.6 + - - +
589B VAL* 3.5 0.7 - - - -
590B SER* 2.9 45.4 + - - -
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Residues in contact with ILE 576 (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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437B LEU* 3.7 38.6 - - + -
551B LEU* 3.8 16.6 - - + -
552B SER 2.8 11.3 + - - -
553B THR* 3.1 35.7 - - + -
554B ALA 3.2 4.3 + - - +
566B PHE* 3.5 3.5 - - - -
574B TYR* 4.3 4.7 - - + -
575B GLY* 1.3 78.2 - - - +
577B CYS* 1.3 65.4 + - - +
578B TYR* 4.4 14.2 - - + -
587B PHE* 4.5 12.6 - - + -
588B SER 3.3 7.6 - - - +
589B VAL* 4.1 20.6 - - + -
603B MET* 4.3 14.8 - - + -
607B LEU* 4.8 6.5 - - + -
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Residues in contact with CYS 577 (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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554B ALA 3.5 6.3 - - - -
556B VAL* 3.5 33.2 - - - -
563B VAL* 3.9 1.8 - - - +
564B GLY* 3.2 37.5 - - - +
565B PHE* 4.1 0.9 - - - -
566B PHE* 3.7 14.6 - - + +
575B GLY 4.2 0.2 - - - -
576B ILE* 1.3 75.4 - - - +
578B TYR* 1.3 68.6 + - - +
587B PHE* 3.5 1.7 - - - -
588B SER* 2.9 36.2 + - - +
1702B HC5 3.7 10.3 - - - -
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Residues in contact with TYR 578 (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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430B ASP* 2.6 30.8 + - - -
433B ILE* 3.8 34.5 - - + -
434B GLN* 2.7 33.5 + - - +
437B LEU* 6.2 0.9 - - + -
453B GLU* 3.2 3.6 + - - -
553B THR* 4.6 4.3 - - + -
554B ALA 3.3 19.3 + - - -
555B GLN* 3.4 21.7 + - + -
556B VAL* 2.8 28.1 + - - -
563B VAL* 4.2 4.5 - - - -
576B ILE* 4.4 8.1 - - + -
577B CYS* 1.3 81.7 - - - +
579B ASN* 1.3 59.0 + - - +
580B PRO* 3.6 8.1 - - + +
585B ILE* 4.2 2.5 - - + -
586B ASN 3.0 14.4 - - - +
587B PHE* 3.4 25.4 - + + -
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Residues in contact with ASN 579 (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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556B VAL 3.4 17.4 - - - +
557B PRO* 3.7 2.8 - - - +
558B ALA* 3.3 22.7 + - - +
560B THR 3.3 20.6 + - - -
562B CYS* 2.7 31.6 + - - +
563B VAL* 4.3 4.0 - - - +
578B TYR* 1.3 72.5 - - - +
580B PRO* 1.3 68.9 - - - +
581B MET* 3.2 26.9 + - - +
585B ILE* 3.7 1.1 - - - -
586B ASN* 2.9 31.8 + - + +
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Residues in contact with PRO 580 (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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419B LYS* 3.6 32.9 + - + +
429B PRO* 5.3 2.7 - - + -
433B ILE* 3.9 22.4 - - + -
555B GLN* 3.5 44.6 - - + +
557B PRO* 4.6 8.3 - - + +
578B TYR* 3.6 4.9 - - + +
579B ASN* 1.3 89.9 - - - +
581B MET* 1.3 64.4 + - - +
585B ILE* 3.9 13.9 - - + -
1701B COA 6.4 0.7 - - - -
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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