Contacts of the strand formed by residues 451 - 455 (chain D) in PDB entry 2DB3
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 VAL 451 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235D VAL* 4.2 4.3 - - + -
236D THR 3.5 10.5 - - - +
237D GLY* 5.4 0.4 - - - -
240D VAL* 3.9 34.5 - - + -
241D PRO* 5.2 0.2 - - + -
278D VAL* 3.8 32.1 - - + -
283D ARG* 4.0 28.0 - - + +
284D ASP 3.0 11.0 + - - +
285D LEU* 3.3 8.4 - - + +
286D MET 2.9 26.2 + - - -
450D TYR* 1.3 77.2 - - - +
452D PHE* 1.3 70.6 + - - +
453D VAL* 4.1 3.6 - - + -
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Residues in contact with PHE 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D LYS* 3.8 23.6 - - + -
235D VAL* 3.3 7.1 - - - +
236D THR* 2.8 60.7 + - + +
286D MET* 3.6 23.3 - - - -
288D CYS* 3.9 23.8 - - - -
440D GLN* 3.4 25.6 - - - -
450D TYR* 4.0 13.6 + + + -
451D VAL* 1.3 73.8 - - - +
453D VAL* 1.3 62.9 + - - +
454D ALA* 3.8 30.7 - - + -
458D VAL* 4.3 9.0 - - + -
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Residues in contact with VAL 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D VAL* 5.0 0.2 - - + -
234D LYS 3.4 7.0 - - - +
235D VAL* 4.5 6.5 - - + +
271D ILE* 3.8 7.9 - - + -
274D CYS* 3.8 30.5 - - + -
275D SER* 4.3 4.0 - - - +
285D LEU* 3.6 11.9 - - + -
286D MET 3.0 6.9 + - - +
287D ALA* 3.3 31.7 - - + -
288D CYS* 2.8 29.1 + - - +
451D VAL* 5.1 4.9 - - + -
452D PHE* 1.3 76.7 - - - +
454D ALA* 1.3 63.3 + - - +
455D ILE* 4.0 18.8 - - + -
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Residues in contact with ALA 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D PRO 3.9 0.2 - - - +
233D VAL* 3.8 0.3 - - - -
234D LYS* 2.8 47.5 + - + +
288D CYS* 3.4 5.4 - - + -
452D PHE* 3.8 22.6 - - + -
453D VAL* 1.3 73.8 - - - +
455D ILE* 1.3 64.1 + - - +
456D GLY 3.5 8.6 + - - +
458D VAL* 3.8 24.9 - - + -
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Residues in contact with ILE 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ILE* 4.0 24.4 - - + +
232D PRO 3.9 2.2 - - - -
233D VAL* 4.1 22.7 - - + +
270D PRO* 3.8 41.5 - - + +
271D ILE* 3.8 13.5 - - + +
274D CYS* 4.5 1.3 - - - -
288D CYS 2.8 21.8 + - - +
289D ALA* 3.7 25.3 - - + -
290D GLN* 4.5 8.8 + - + +
293D SER* 6.5 0.4 - - - -
453D VAL* 4.0 19.5 - - + -
454D ALA* 1.3 71.3 - - - +
456D GLY* 1.3 63.7 + - - +
457D ILE 4.6 2.8 - - - +
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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