Contacts of the strand formed by residues 561 - 567 (chain A) in PDB entry 2CG2
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 LEU 561 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A LYS* 5.8 0.7 - - + -
560A ALA* 1.3 78.0 - - - +
562A SER* 1.3 62.7 + - - +
563A ILE* 3.8 27.6 - - + -
576A LEU* 5.3 1.6 - - + +
577A GLU* 3.6 1.4 - - - +
578A LEU* 2.8 53.8 + - + +
583A LEU* 5.7 0.4 - - + -
632A LEU* 3.8 35.4 - - + +
635A GLN* 3.9 22.4 - - + +
636A LEU* 4.3 20.0 - - + +
639A MET* 4.4 13.7 - - + -
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Residues in contact with SER 562 (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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561A LEU* 1.3 76.6 - - - +
563A ILE* 1.3 68.8 + - - +
575A LEU* 4.5 5.2 - - - -
576A LEU 3.1 11.0 - - - -
577A GLU* 3.9 16.6 - - - -
591A SER* 5.5 0.8 + - - -
593A ASP 3.7 5.7 + - - -
594A ALA* 3.1 22.0 + - - -
595A GLY* 2.9 28.2 + - - +
596A GLN 3.5 3.1 + - - -
632A LEU* 4.0 2.5 - - - +
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Residues in contact with ILE 563 (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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561A LEU* 3.8 23.1 - - + -
562A SER* 1.3 80.9 - - - +
564A ASN* 1.3 77.2 + - - +
565A LEU* 3.6 3.9 + - + +
575A LEU* 3.7 4.6 - - - +
576A LEU* 2.8 53.1 + - + +
596A GLN* 3.2 13.7 - - + +
598A VAL* 3.9 20.6 - - + -
632A LEU* 3.9 9.2 - - + +
633A LEU* 3.6 41.3 - - + +
636A LEU* 4.3 13.5 - - + -
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Residues in contact with ASN 564 (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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563A ILE* 1.3 73.3 - - - +
565A LEU* 1.3 54.3 + - - +
574A TYR 3.6 3.8 - - - -
575A LEU* 3.4 11.6 - - - +
590A GLN* 3.0 33.0 - - - +
591A SER 2.7 47.5 + - - +
594A ALA* 3.4 10.8 - - - +
596A GLN 2.9 7.3 + - - -
597A THR* 3.4 22.5 + - + +
598A VAL 2.7 32.6 + - - +
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Residues in contact with LEU 565 (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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544A PHE* 3.4 41.3 - - + -
563A ILE* 3.6 2.2 + - + -
564A ASN* 1.3 72.8 - - - +
566A ARG* 1.3 61.8 + - - +
567A LEU* 3.7 28.0 - - + +
572A GLU 4.1 0.5 - - - +
573A ASN* 3.2 4.0 - - - -
574A TYR* 2.7 48.5 + - + +
576A LEU* 4.5 15.5 - - + -
590A GLN* 3.8 1.2 - - - +
598A VAL* 3.4 21.8 - - + +
600A ILE* 3.8 25.4 - - + -
605A LEU* 4.5 4.3 - - + -
633A LEU* 5.2 9.4 - - + -
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Residues in contact with ARG 566 (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 LEU* 1.3 73.1 - - - +
567A LEU* 1.3 62.3 + - - +
568A PRO* 3.5 4.7 - - + +
572A GLU 3.8 3.8 - - - -
573A ASN* 3.3 39.4 + - - +
590A GLN* 3.1 35.9 - - - +
597A THR* 4.1 18.5 - - + +
598A VAL 2.7 15.1 + - - +
599A SER* 3.2 14.9 - - - +
600A ILE* 2.9 28.9 + - - +
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Residues in contact with LEU 567 (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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540A THR* 4.2 7.6 - - + -
565A LEU* 3.7 27.6 - - + +
566A ARG* 1.3 76.7 - - - +
568A PRO* 1.3 61.8 - - - +
569A ASP* 3.4 2.5 - - - -
570A ILE* 3.4 14.8 + - + +
571A GLY 2.9 21.3 + - - -
572A GLU* 2.8 28.1 + - + +
573A ASN* 4.5 0.6 + - - -
574A TYR* 4.1 20.4 - - + -
600A ILE* 3.0 10.8 - - + +
601A ASP 4.4 0.7 - - - +
602A ARG* 3.6 42.8 - - + +
605A LEU* 3.9 18.6 - - + -
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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