Contacts of the strand formed by residues 565 - 570 (chain B) in PDB entry 3GUT
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 GLU 565 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ARG* 3.9 9.4 + - - -
200A ASN* 5.9 0.7 - - - -
554B ASP* 4.6 4.0 - - - +
555B ARG* 5.6 0.5 - - - +
563B GLY 3.5 1.8 + - - +
564B GLU* 1.3 70.6 - - - +
566B ILE* 1.3 71.7 + - - +
567B TYR* 4.2 13.5 - - + -
610B VAL* 2.8 31.3 - - + +
611B PHE 3.1 10.8 - - - +
612B LYS* 3.9 20.3 - - + -
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Residues in contact with ILE 566 (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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553B MET* 3.9 17.9 - - + -
554B ASP* 3.7 11.7 - - - +
555B ARG* 3.8 33.7 - - + +
557B ALA 5.5 1.8 - - - +
564B GLU* 3.4 24.9 - - + +
565B GLU* 1.3 81.3 - - - +
567B TYR* 1.3 75.0 + - - +
609B ILE 3.5 0.3 - - - +
610B VAL* 3.5 2.4 - - - +
611B PHE* 2.6 67.2 + - + -
613B THR* 3.7 19.1 - - - +
645B PHE* 5.2 4.7 - - + -
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Residues in contact with TYR 567 (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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198A ARG* 3.5 16.7 + - + +
199A VAL 3.2 27.4 + - - -
200A ASN* 3.6 31.4 - - + -
213A PHE* 3.8 31.4 - - + -
215A LEU* 4.1 35.7 - - + -
553B MET* 3.6 3.1 - - - -
554B ASP* 3.3 39.0 + - - +
565B GLU* 4.2 15.7 - - + -
566B ILE* 1.3 79.8 - - - +
568B LEU* 1.3 62.3 + - - +
569B LEU* 5.2 1.3 - - + -
609B ILE 3.7 2.9 - - - -
610B VAL* 3.7 28.7 - - + -
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Residues in contact with LEU 568 (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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550B ILE* 3.3 31.0 - - + -
552B ARG 4.0 2.5 - - - -
553B MET* 3.8 16.4 - - + -
566B ILE 4.0 0.2 + - - -
567B TYR* 1.3 74.8 - - - +
569B LEU* 1.3 72.0 + - - +
570B CYS* 3.8 18.2 - - + -
580B ILE* 5.1 7.2 - - + -
608B ALA* 2.7 14.1 - - - +
609B ILE* 2.6 60.4 + - + +
611B PHE* 3.9 20.6 - - + -
629B VAL* 6.1 2.0 - - + -
631B LEU* 4.4 12.8 - - + -
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Residues in contact with LEU 569 (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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213A PHE* 3.8 21.3 - - + -
215A LEU* 4.2 7.2 - - + -
245A HIS* 3.5 30.3 - - + +
249A ALA* 4.0 18.6 - - + -
251A VAL* 3.7 30.5 - - + -
550B ILE 3.9 0.3 - - - -
551B VAL* 3.0 23.7 + - + -
552B ARG* 3.2 29.0 + - + +
567B TYR* 5.2 1.1 - - + -
568B LEU* 1.3 81.1 - - - +
570B CYS* 1.3 60.8 + - - +
607B PHE 3.4 2.0 - - - -
608B ALA* 3.2 25.6 - - + -
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Residues in contact with CYS 570 (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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245A HIS* 2.7 30.2 + - - -
246A ARG* 4.6 0.2 + - - -
549B LYS 3.5 16.2 - - - +
551B VAL* 4.2 3.1 - - - +
568B LEU* 3.8 15.3 - - + -
569B LEU* 1.3 75.8 - - - +
571B ASP* 1.3 69.9 + - - +
573B VAL* 3.5 30.1 - - - -
607B PHE* 2.7 40.8 + - - +
608B ALA* 3.6 8.7 - - - -
609B ILE* 4.5 3.8 - - - -
631B LEU* 4.1 9.2 - - + -
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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