Contacts of the strand formed by residues 563 - 569 (chain A) in PDB entry 3CMM
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 563 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A VAL 3.4 15.9 - - - +
541A ASN* 3.6 36.8 - - - +
549A ARG 5.3 0.2 - - - +
552A VAL* 4.1 10.1 - - + -
553A ASP* 3.7 42.0 - - + +
556A CYS* 3.9 15.9 - - + -
561A LYS 3.6 0.4 + - - +
562A PRO* 1.3 74.6 - - - +
564A LEU* 1.3 68.7 + - - +
565A GLU* 4.7 4.9 - - + +
577A VAL* 3.7 3.5 - - - +
578A ILE* 2.9 56.4 + - + +
586A TYR* 4.9 1.3 - - + -
884A LEU* 5.6 0.4 - - - +
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Residues in contact with LEU 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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538A PHE* 4.2 2.0 - - + -
539A VAL 2.9 10.2 + - - +
540A THR* 3.8 24.1 - - + +
541A ASN* 2.8 33.1 + - - +
563A LEU* 1.3 73.3 - - - +
565A GLU* 1.3 59.9 + - - +
576A GLN 4.0 0.7 - - - +
577A VAL* 3.4 31.0 - - + -
877A VAL* 3.8 29.6 - - + +
880A GLU* 4.3 13.0 - - + -
881A LEU* 4.0 28.5 - - + -
884A LEU* 3.8 29.8 - - + -
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Residues in contact with GLU 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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541A ASN* 2.7 36.8 - - + +
549A ARG* 2.9 31.6 + - - +
563A LEU* 3.8 4.5 + - + -
564A LEU* 1.3 73.7 - - - +
566A SER* 1.3 92.5 + - - +
574A ASN* 5.0 5.1 + - - -
575A THR* 3.5 2.9 + - - +
576A GLN* 2.8 49.0 + - + +
578A ILE* 4.4 11.0 - - + -
586A TYR* 3.7 27.5 - - + -
877A VAL* 4.3 4.5 - - - +
73B LEU 5.4 0.5 - - - +
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Residues in contact with SER 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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445A ILE* 3.8 28.3 - - - +
541A ASN 3.9 10.2 + - - +
543A LEU 4.6 1.2 + - - +
549A ARG* 2.9 17.7 + - - -
565A GLU* 1.3 90.3 + - - +
567A GLY* 1.3 59.0 + - - +
574A ASN* 3.2 11.7 - - - +
575A THR* 4.2 0.7 - - - +
873A VAL* 3.5 22.2 - - - -
877A VAL* 3.7 17.5 - - - +
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Residues in contact with GLY 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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445A ILE* 4.2 3.1 - - - -
549A ARG* 3.5 8.3 - - - -
566A SER* 1.3 75.7 - - - +
568A THR* 1.3 69.3 + - - +
574A ASN* 3.0 33.7 + - - +
873A VAL* 4.2 0.7 - - - +
73B LEU* 3.1 23.1 - - - -
75B GLY 3.6 3.1 - - - -
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Residues in contact with THR 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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445A ILE* 4.1 15.0 - - + -
567A GLY* 1.3 80.4 - - - +
569A LEU* 1.3 61.6 + - - +
570A GLY 4.9 2.0 + - - -
572A LYS 3.2 10.8 - - - -
863A ILE* 4.0 4.0 - - - +
865A ALA* 4.8 12.5 - - - +
866A ILE 5.8 0.2 + - - -
869A THR* 3.9 31.4 - - + +
870A THR* 4.3 12.5 + - - +
873A VAL* 4.1 12.6 - - + -
73B LEU* 3.8 5.9 + - - -
74B ARG 2.8 21.5 - - - +
75B GLY 2.8 21.0 + - - +
76B GLY* 4.4 3.8 - - - -
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Residues in contact with LEU 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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568A THR* 1.3 76.3 - - - +
570A GLY* 1.3 64.2 + - - +
571A THR 3.2 0.5 + - - -
572A LYS* 2.7 42.7 + - + +
863A ILE* 4.1 11.0 - - + -
864A PRO* 3.8 34.5 - - + -
73B LEU* 3.7 26.6 - - + +
74B ARG* 4.6 17.0 - - + +
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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