Contacts of the strand formed by residues 570 - 575 (chain A) in PDB entry 1CJY
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 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A PRO* 6.2 0.2 - - + -
189A VAL 3.5 2.1 + - - +
190A VAL* 3.4 21.5 - - + +
191A ALA 3.0 24.4 + - - -
568A VAL* 3.6 1.0 - - - +
569A ASP* 1.3 89.7 + - - +
571A ILE* 1.3 62.6 + - - +
572A ILE* 4.1 20.9 - - + -
636A THR* 3.6 26.9 - - + +
638A ILE* 4.4 11.4 - - + -
708A ILE* 4.8 1.8 - - + +
711A ALA* 3.9 16.8 - - + -
712A MET* 3.6 40.8 - - + +
715A SER* 3.9 7.4 - - - +
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Residues in contact with ILE 571 (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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191A ALA 3.6 2.9 - - - -
193A LEU* 3.8 20.0 - - + -
558A TYR* 3.8 20.4 - - + +
561A ILE* 3.4 35.9 - - + +
562A LEU* 3.7 24.0 - - + -
568A VAL* 3.7 17.0 - - + -
570A LEU* 1.3 72.0 - - - +
572A ILE* 1.3 60.5 + - - +
573A SER 3.4 5.8 + - - +
635A PRO* 3.8 24.0 - - + -
636A THR 2.9 12.5 + - - +
637A ILE* 3.4 7.3 - - + +
638A ILE 2.9 25.9 + - - +
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Residues in contact with ILE 572 (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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190A VAL* 3.7 28.3 - - + -
191A ALA 2.9 12.1 + - - +
192A ILE* 3.7 7.3 - - + -
193A LEU 3.2 12.9 + - - -
212A LEU* 5.3 2.5 - - + -
217A ILE* 4.5 12.3 - - + -
570A LEU* 4.1 14.6 - - + -
571A ILE* 1.3 71.0 - - - +
573A SER* 1.3 55.7 + - - +
574A PHE* 3.1 37.8 - - + -
638A ILE* 3.7 10.1 - - + +
640A PHE* 4.1 15.9 - - + -
708A ILE* 3.5 40.8 - - + -
712A MET* 4.9 0.7 - - + -
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Residues in contact with SER 573 (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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193A LEU* 3.7 20.3 - - - +
556A LEU* 3.9 22.2 - - - +
558A TYR* 3.8 22.2 + - - -
571A ILE* 3.4 3.4 + - - +
572A ILE* 1.3 70.4 - - - +
574A PHE* 1.3 70.1 + - - +
637A ILE* 4.6 0.7 - - - -
638A ILE 2.9 14.1 + - - +
639A HIS* 4.2 15.2 + - - -
640A PHE* 2.9 30.6 + - - +
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Residues in contact with PHE 574 (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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192A ILE* 4.4 4.7 - - + -
193A LEU 2.7 18.7 + - - +
194A GLY 3.7 0.3 - - - -
195A SER* 3.1 27.5 + - - -
205A PHE* 4.6 3.4 - + + -
208A VAL* 3.4 41.3 - - + -
212A LEU* 4.3 13.7 - - + -
556A LEU* 4.4 0.7 - - - +
572A ILE* 3.1 43.1 - - + -
573A SER* 1.3 77.3 + - - +
575A ASP* 1.3 59.8 + - - +
576A PHE* 3.8 19.7 - - + -
640A PHE* 3.6 35.2 - + + -
697A MET* 4.2 5.8 - - + -
701A THR* 3.5 24.5 - - + -
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Residues in contact with ASP 575 (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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195A SER* 3.6 7.1 + - - -
556A LEU* 4.1 7.2 - - + -
573A SER* 4.2 0.4 - - - +
574A PHE* 1.3 72.5 - - - +
576A PHE* 1.3 62.7 + - - +
577A SER* 2.5 42.0 + - - +
586A PRO* 4.4 2.5 - - - +
589A GLU* 2.5 44.2 - - - +
639A HIS* 3.8 14.1 + - + +
640A PHE 3.0 18.8 + - - +
641A VAL* 3.9 5.4 - - + +
642A LEU* 3.2 27.0 + - - +
697A MET* 5.6 0.5 - - - +
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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