Contacts of the strand formed by residues 576 - 582 (chain A) in PDB entry 2RC4
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 576 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571A TYR* 4.2 4.3 - - + -
572A ARG* 3.7 0.3 - - - -
573A LYS 3.1 31.8 + - - +
574A ASN* 4.2 0.9 - - - +
575A ASN* 1.3 76.0 - - - +
577A SER* 1.3 67.5 + - - +
618A LEU* 4.3 15.3 - - + -
619A THR 3.4 8.1 - - - +
620A GLN* 4.8 2.2 - - - +
658A TYR* 5.1 8.1 - - + -
661A PHE* 5.0 13.5 - - + -
767A VAL* 5.1 13.5 - - + -
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Residues in contact with SER 577 (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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569A GLU* 3.6 18.3 + - - -
571A TYR* 3.2 16.4 - - - -
572A ARG* 4.2 4.0 - - - +
574A ASN 5.2 0.9 + - - -
575A ASN 3.7 0.9 + - - -
576A ILE* 1.3 80.9 + - - +
578A VAL* 1.3 61.6 + - - +
579A PHE* 4.0 6.3 - - - -
617A VAL 3.6 0.7 - - - +
618A LEU* 3.2 5.7 - - - +
619A THR* 2.7 48.4 + - - -
621A ASN* 3.1 23.6 + - - -
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Residues in contact with VAL 578 (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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569A GLU* 3.6 3.5 - - - +
570A ILE* 3.0 30.6 + - + +
571A TYR* 2.9 22.5 + - + +
577A SER* 1.3 78.4 - - - +
579A PHE* 1.3 65.7 + - - +
616A TYR* 5.3 3.8 - - + -
617A VAL 3.2 6.1 - - - +
618A LEU* 3.8 29.4 - - + +
661A PHE* 4.1 11.9 - - + -
662A LEU* 4.3 9.6 - - + -
665A PHE* 3.2 40.8 - - + -
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Residues in contact with PHE 579 (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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564A HIS* 3.8 23.1 - + + -
565A PRO* 3.6 49.8 - - + -
567A ALA 4.3 8.1 - - - +
568A ASN 3.5 7.2 - - - +
569A GLU* 3.4 37.5 - - + -
570A ILE* 4.7 1.6 - - - -
577A SER* 4.0 11.2 - - - -
578A VAL* 1.3 77.4 - - - +
580A GLU* 1.3 59.2 + - - +
581A VAL* 3.4 6.4 + - + -
615A PHE 3.3 2.8 - - - +
616A TYR* 3.3 4.0 - - - -
617A VAL* 2.8 40.4 + - + +
619A THR* 3.3 24.2 - - + -
626A CYS* 4.2 15.7 - - + -
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Residues in contact with GLU 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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567A ALA* 2.7 23.5 - - - +
568A ASN 3.3 8.9 + - - +
570A ILE* 3.6 30.7 - - + +
578A VAL 4.1 1.4 + - - -
579A PHE* 1.3 67.9 - - - +
581A VAL* 1.3 56.3 + - - +
582A ASP* 3.7 2.5 + - + +
614A LEU* 3.4 20.1 - - + +
615A PHE 3.7 2.5 - - - -
616A TYR* 2.9 34.5 + - + +
776A TRP* 2.7 33.4 + - - -
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Residues in contact with VAL 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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565A PRO* 4.4 2.9 - - + -
566A PRO* 3.7 15.7 - - + -
567A ALA* 3.5 26.7 - - + +
579A PHE* 4.3 12.8 - - + +
580A GLU* 1.3 72.6 - - - +
582A ASP* 1.3 63.4 + - - +
583A GLY 3.6 0.2 + - - -
586A SER* 3.7 17.5 - - - +
589A TYR* 4.2 15.3 - - + -
590A CYS* 3.4 27.8 - - - -
614A LEU* 3.5 1.3 - - - -
615A PHE* 2.5 52.2 + - + +
617A VAL* 4.7 2.5 - - + -
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Residues in contact with ASP 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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567A ALA* 4.5 3.4 - - - +
580A GLU* 3.7 5.9 + - + +
581A VAL* 1.3 76.4 - - - +
583A GLY* 1.3 72.6 + - - +
584A ASN* 3.1 12.5 + - - +
585A VAL* 3.0 38.0 + - + +
586A SER* 3.2 24.9 + - - -
613A PHE 4.1 1.1 - - - +
614A LEU* 4.1 11.1 - - + +
636A LYS* 2.8 35.5 + - - -
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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