Contacts of the strand formed by residues 526 - 532 (chain C) in PDB entry 3CB4
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 526 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487C ILE* 4.8 5.8 - - + -
488C ASN* 3.4 22.7 - - - +
519C ILE* 3.6 22.4 - - + -
520C PRO 4.8 1.1 - - - +
522C GLN* 3.4 41.5 - - + +
524C PHE 3.9 9.9 - - - +
525C ASP* 1.3 79.2 - - - +
527C ALA* 1.3 63.7 + - - +
528C ILE* 3.6 21.7 + - + -
540C SER 3.9 0.2 - - - +
541C THR* 3.2 5.3 + - - -
542C VAL* 2.8 45.1 + - + +
550F LEU* 3.8 15.5 - - + -
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Residues in contact with ALA 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486C LEU 3.5 3.5 - - - +
487C ILE* 3.2 3.6 - - - -
488C ASN* 2.8 40.2 + - - +
489C GLY 4.5 2.3 + - - +
525C ASP 4.2 0.6 - - - -
526C ILE* 1.3 70.7 - - - +
528C ILE* 1.3 61.5 + - - +
529C GLN* 4.6 14.7 + - - +
539C ARG* 5.3 8.7 - - - -
540C SER 4.1 3.1 - - - -
541C THR* 4.3 10.5 - - - -
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Residues in contact with ILE 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485C VAL* 4.6 3.8 - - + -
487C ILE* 3.6 25.8 - - + -
512C VAL* 3.8 25.1 - - + +
515C MET* 3.7 37.9 - - + -
516C LYS* 4.2 6.3 - - + +
519C ILE* 4.0 13.9 - - + -
526C ILE* 3.9 12.8 - - + +
527C ALA* 1.3 74.7 - - - +
529C GLN* 1.3 63.5 + - - +
539C ARG* 3.3 3.8 - - - +
540C SER 2.9 39.6 + - - +
542C VAL* 3.8 25.6 - - + -
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Residues in contact with GLN 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C ASP 3.8 0.2 - - - +
485C VAL* 3.4 6.6 - - - +
486C LEU* 3.0 72.9 + - + +
489C GLY* 5.6 4.0 - - - +
512C VAL* 4.3 3.6 - - - -
527C ALA* 4.6 13.2 + - - +
528C ILE* 1.3 80.4 - - - +
530C ALA* 1.3 61.9 + - - +
536C ILE* 3.2 33.3 - - + +
538C ALA 3.2 12.1 - - - +
539C ARG* 2.8 35.3 - - + +
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Residues in contact with ALA 530 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483C VAL* 3.8 10.5 - - + -
484C ASP 3.4 5.8 - - - -
485C VAL* 4.6 3.8 - - + +
508C GLY* 3.5 39.5 - - - +
511C LEU* 5.3 2.5 - - + -
512C VAL* 3.7 7.1 - - + +
529C GLN* 1.3 73.9 - - - +
531C ALA* 1.3 62.3 + - - +
536C ILE* 3.5 5.0 - - - +
537C ILE* 3.1 28.3 + - + -
538C ALA* 2.9 12.8 + - + +
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Residues in contact with ALA 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C ARG 3.8 0.3 - - - +
483C VAL* 3.3 10.2 - - - +
484C ASP* 2.9 37.3 + - + +
486C LEU* 4.2 18.2 - - + -
529C GLN 5.4 0.2 - - - -
530C ALA* 1.3 77.9 - - - +
532C ILE* 1.3 62.4 + - - +
533C GLY 3.9 14.8 - - - +
534C THR 5.2 0.9 - - - +
535C HIS 3.3 15.9 - - - +
536C ILE* 4.2 7.0 - - + -
537C ILE* 4.3 3.1 - - - +
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Residues in contact with ILE 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C VAL* 4.4 20.0 - - + -
482C ARG 4.0 11.9 - - - +
483C VAL* 3.9 13.7 - - + -
501C ARG* 5.2 7.4 - - - +
504C SER* 3.6 33.2 - - - +
531C ALA* 1.3 77.0 - - - +
533C GLY* 1.3 66.3 + - - +
534C THR 3.4 0.2 + - - -
535C HIS* 2.8 31.1 + - - +
537C ILE* 4.2 16.7 - - + +
165E THR* 3.9 21.1 - - + -
167E VAL* 4.5 12.8 - - + +
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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