Contacts of the strand formed by residues 640 - 645 (chain B) in PDB entry 2A2N
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 640 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B ILE* 4.1 20.2 - - + -
497B HIS 3.4 6.1 - - - +
498B THR* 4.4 0.9 - - + +
528B TYR* 3.4 35.2 - - + +
530B GLY* 2.6 35.2 + - - -
531B HIS* 2.6 14.9 + - + +
533B PHE* 4.3 11.9 - - + -
544B THR* 3.5 36.1 - - + +
545B GLY 4.9 0.4 - - - +
592B PHE* 4.5 3.8 - - + -
638B VAL 4.4 0.2 + - - -
639B SER* 1.3 71.3 - - - +
641B ILE* 1.3 59.6 + - - +
642B ASN* 3.7 28.3 - - - +
643B ILE* 3.8 11.9 - - + -
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Residues in contact with ILE 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B HIS* 2.7 24.3 + - + +
498B THR 3.3 33.0 - - - +
499B SER* 4.0 6.3 - - - +
502B ASP* 5.4 1.1 - - - +
529B ASN* 3.4 15.8 + - - +
530B GLY 3.9 1.0 + - - -
639B SER* 3.3 6.5 + - - +
640B ILE* 1.3 75.5 - - - +
642B ASN* 1.3 74.4 + - - +
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Residues in contact with ASN 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B HIS* 2.9 56.5 + - - +
529B ASN* 3.2 27.8 - - - +
640B ILE* 3.8 3.1 - - - +
641B ILE* 1.3 89.8 - - + +
643B ILE* 1.3 69.9 + - - +
644B THR* 4.1 10.9 + - - +
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Residues in contact with ILE 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B ALA* 4.1 17.7 - - + -
495B ILE 3.3 16.6 - - - +
496B ILE* 4.0 18.8 - - + +
519B PHE* 4.1 17.3 - - + -
523B SER* 3.6 40.3 + - - +
524B ARG* 5.1 1.2 - - - -
528B TYR* 3.5 41.3 - - + -
529B ASN* 3.8 4.0 + - - +
592B PHE* 4.7 1.8 - - + -
640B ILE* 3.8 14.1 - - + -
642B ASN* 1.3 83.7 + - - +
644B THR* 1.3 64.3 + - - +
645B VAL* 3.9 1.7 + - - +
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Residues in contact with THR 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B ALA* 3.0 5.4 - - - +
495B ILE* 2.7 49.7 + - + +
497B HIS* 3.2 23.7 + - - -
642B ASN* 4.1 8.1 + - - -
643B ILE* 1.3 72.2 - - - +
645B VAL* 1.3 70.5 + - - +
646B LYS* 4.1 2.0 + - - +
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Residues in contact with VAL 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A TRP* 6.0 1.0 - - - +
491B SER* 3.4 29.6 - - - -
493B SER 3.5 8.5 - - - +
494B ALA* 4.6 5.8 - - + -
519B PHE* 5.7 0.4 - - + -
520B CYS* 3.8 27.1 - - - +
523B SER* 3.7 30.5 - - - +
524B ARG* 3.8 30.6 + - + +
643B ILE 3.9 1.3 + - - +
644B THR* 1.3 82.0 - - - +
646B LYS* 1.3 64.2 + - - +
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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