Contacts of the strand formed by residues 578 - 582 (chain A) in PDB entry 2D2O
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 GLY 578 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A LEU* 4.1 8.3 - - - +
441A LEU* 3.7 24.6 - - - +
531A VAL 3.1 9.4 - - - -
532A LEU* 4.3 2.0 - - - -
555A ASP* 4.5 1.4 - - - +
557A LEU* 3.6 16.3 - - - +
576A TYR 4.1 0.8 + - - -
577A GLN* 1.3 85.8 + - - +
579A MET* 1.3 65.0 + - - +
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Residues in contact with MET 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A LEU* 5.1 0.2 - - - +
530A VAL* 3.3 10.4 - - - +
531A VAL* 2.8 34.7 + - + +
555A ASP* 3.5 31.2 - - + +
558A THR* 5.6 0.2 - - - +
560A GLU* 3.0 29.8 - - - +
571A LEU* 4.0 34.5 - - + -
572A THR 4.6 10.3 - - - +
573A LEU* 3.4 28.7 - - + -
577A GLN* 4.4 11.9 - - - +
578A GLY* 1.3 74.8 - - - +
580A ILE* 1.3 65.8 + - - +
581A LEU* 3.8 16.2 - - + -
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Residues in contact with ILE 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A LEU* 4.3 8.3 - - + -
445A THR* 3.8 29.6 - - + -
490A LEU* 3.9 12.6 - - + -
493A LEU* 3.9 15.5 - - + -
497A LEU* 4.2 18.2 - - + -
500A LEU* 4.9 2.5 - - + -
528A VAL* 3.8 22.2 - - + -
529A GLY 3.8 2.9 - - - -
530A VAL* 4.8 2.9 - - + +
554A LEU 3.2 1.6 - - - +
555A ASP* 3.1 12.6 + - - +
556A CYS* 2.9 30.4 + - + +
557A LEU* 3.7 30.5 - - + -
579A MET* 1.3 77.4 - - - +
581A LEU* 1.3 58.5 + - - +
582A TRP 3.5 0.9 + - - -
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Residues in contact with LEU 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508A TRP* 4.0 20.2 - - + -
528A VAL* 3.2 5.1 - - - -
529A GLY* 2.8 40.4 + - - +
531A VAL* 4.1 8.3 - - + -
553A TRP* 3.3 26.6 - - + -
554A LEU 3.3 4.0 - - - +
555A ASP* 3.8 30.7 - - + +
562A VAL* 4.4 16.6 - - + -
569A LEU* 5.6 4.5 - - + -
571A LEU* 3.9 30.3 - - + -
579A MET* 4.2 17.9 - - + -
580A ILE* 1.3 68.4 - - - +
582A TRP* 1.3 60.5 + - - +
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Residues in contact with TRP 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A LEU* 3.8 21.3 - - + +
526A GLN* 3.6 8.7 - - + +
527A HIS 3.8 1.8 - - - -
528A VAL* 3.9 17.3 - - + -
553A TRP* 3.4 3.1 - - - -
554A LEU* 2.8 57.9 + - + +
556A CYS* 3.6 24.0 - - - -
580A ILE 3.5 0.4 + - - -
581A LEU* 1.3 73.1 - - - +
583A ASN* 1.3 69.4 + - - +
584A GLY* 3.1 43.5 + - - -
585A ARG 2.7 27.7 + - - +
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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