Contacts of the strand formed by residues 563 - 570 (chain A) in PDB entry 4JPB
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 563 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A LEU* 3.6 44.2 - - + -
558A ILE* 4.2 14.8 - - + +
559A PRO 3.8 13.0 - - - +
560A ILE* 3.2 16.7 + - + +
561A ALA 4.9 0.3 - - - -
562A ASN* 1.3 79.8 - - - +
564A ASP* 1.3 63.3 + - - +
565A THR 3.3 22.9 - - - +
566A ILE* 4.2 1.3 - - + -
613A VAL* 4.0 13.2 - - + -
614A ILE 3.6 7.2 - - - +
615A VAL* 4.4 0.9 - - - +
616A ARG* 3.8 10.5 + - - -
142B ILE* 3.7 29.7 - - + +
146B ARG* 4.1 11.1 + - - -
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Residues in contact with ASP 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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562A ASN 3.7 0.4 + - - -
563A ILE* 1.3 75.4 - - - +
565A THR* 1.3 86.1 + - + +
614A ILE* 2.8 21.6 + - + +
615A VAL 4.8 5.2 - - - -
616A ARG* 3.1 26.6 + - + +
621A LYS* 3.3 36.5 + - - +
142B ILE* 5.5 0.2 - - - -
146B ARG* 3.4 28.7 + - - +
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Residues in contact with THR 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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563A ILE* 3.3 7.4 - - - +
564A ASP* 1.3 95.2 - - - +
566A ILE* 1.3 92.9 + - - +
567A LEU* 4.1 5.6 + - + +
585A ILE* 5.5 10.3 - - + -
586A ARG* 6.0 3.1 - - - +
614A ILE* 3.1 39.7 + - + -
139B ASN* 3.3 14.2 + - - -
142B ILE* 5.4 2.0 - - - -
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Residues in contact with ILE 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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547A LEU* 3.6 30.3 - - + -
563A ILE* 4.2 8.1 - - + -
565A THR* 1.3 93.9 + - - +
567A LEU* 1.3 65.1 + - - +
612A ALA 3.8 8.5 - - - +
613A VAL* 4.6 5.4 - - + -
629A LEU* 4.1 23.6 - - + -
135B ILE* 3.3 31.3 - - + +
138B LEU* 4.0 24.2 - - + -
139B ASN* 2.9 16.2 + - - +
142B ILE* 3.9 18.6 - - + -
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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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565A THR* 4.8 5.8 - - + +
566A ILE* 1.3 78.3 - - - +
568A SER* 1.3 64.2 + - - +
569A ILE* 4.1 15.9 - - + -
583A ILE* 4.5 6.7 - - + -
585A ILE* 4.1 40.6 - - + -
611A GLU* 3.8 2.6 - - - -
612A ALA* 3.0 52.5 + - + +
614A ILE* 4.0 25.6 - - + -
135B ILE* 4.3 6.3 - - - +
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Residues in contact with SER 568 (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 LEU* 1.3 78.4 - - - +
569A ILE* 1.3 61.0 + - - +
570A SER* 5.1 0.5 + - - -
609A GLU* 3.7 22.4 - - - +
610A MET 3.5 7.2 + - - -
611A GLU* 4.5 0.4 - - - +
131B ARG* 2.3 40.8 + - - -
135B ILE* 4.2 8.2 - - - +
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Residues in contact with ILE 569 (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 LEU* 4.1 11.2 - - + -
568A SER* 1.3 75.5 - - - +
570A SER* 1.3 63.4 + - - +
573A ASP* 4.7 6.3 - - - +
574A ILE* 4.6 14.6 - - + -
583A ILE* 3.6 53.2 - - + -
585A ILE* 5.3 4.7 - - + -
592A VAL* 4.6 4.9 - - + -
609A GLU* 3.6 3.3 - - - -
610A MET* 2.8 42.3 + - + +
612A ALA* 3.9 27.6 - - + -
625A VAL* 4.4 14.1 - - + -
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Residues in contact with SER 570 (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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568A SER 5.1 0.2 + - - -
569A ILE* 1.3 77.9 - - - +
571A LYS* 1.3 68.2 + - - +
572A GLU* 2.8 14.5 + - - +
573A ASP* 2.9 35.2 + - - +
574A ILE* 4.0 6.3 + - - +
608A GLU* 3.1 9.4 - - - -
609A GLU* 3.1 27.7 + - - -
610A MET* 5.0 0.4 - - - -
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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