Contacts of the strand formed by residues 286 - 290 (chain D) in PDB entry 2HU4
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 GLU 286 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282D PRO* 3.3 5.0 - - - +
283D ASN* 2.8 34.7 + - - +
284D ALA 4.3 6.8 - - - +
285D GLY* 1.3 84.4 - - - +
287D ILE* 1.3 71.9 + - - +
288D THR* 5.4 1.3 - - - +
304D SER* 5.3 4.1 + - - -
305D PHE* 3.4 23.7 + - - +
306D ASN* 4.0 20.6 + - - +
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Residues in contact with ILE 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D ALA* 4.1 20.4 - - + -
233D VAL* 4.0 12.3 - - + -
238D PHE* 3.8 34.5 - - + -
280D CYS* 3.7 27.4 - - + -
281D TYR 3.5 6.3 - - - +
282D PRO* 4.9 0.2 - - + -
285D GLY 4.9 1.1 - - - +
286D GLU* 1.3 88.8 - - - +
288D THR* 1.3 64.9 + - - +
289D CYS* 3.9 3.6 - - - -
304D SER* 2.9 26.7 - - - -
305D PHE* 3.0 48.5 + - + +
306D ASN 4.8 2.5 - - - +
308D GLN* 5.4 0.4 - - + -
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Residues in contact with THR 288 (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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279D SER 3.6 1.7 - - - +
280D CYS* 3.2 0.9 - - - -
281D TYR* 2.9 70.5 + - + +
283D ASN* 5.3 4.9 - - - +
286D GLU* 5.4 1.0 - - - +
287D ILE* 1.3 77.7 + - - +
289D CYS* 1.3 69.1 + - - +
290D VAL* 5.0 2.2 - - + -
302D TRP* 5.5 0.7 - - + -
303D VAL 3.5 5.4 - - - +
304D SER* 3.9 11.4 - - - +
355D LYS* 5.1 6.1 - - + +
383D TRP* 4.4 22.9 - - + -
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Residues in contact with CYS 289 (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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240D VAL* 3.9 14.8 - - - -
278D CYS* 4.0 11.0 - - + -
279D SER 3.1 5.2 - - - +
280D CYS* 2.0 46.2 - - - -
287D ILE* 3.9 10.3 - - - -
288D THR* 1.3 75.0 - - - +
290D VAL* 1.3 63.4 + - - +
291D CYS* 4.0 5.4 - - - -
302D TRP* 2.9 30.0 - - - +
303D VAL* 2.6 24.2 + - + +
305D PHE* 4.2 7.6 - - - -
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Residues in contact with VAL 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D SER* 3.0 30.5 + - - +
281D TYR* 5.0 1.3 - - + -
288D THR* 5.0 4.5 - - + -
289D CYS* 1.3 76.2 - - - +
291D CYS* 1.3 62.8 + - - +
300D ARG* 3.6 34.5 - - + -
301D PRO 3.5 4.0 - - - +
302D TRP* 4.4 1.1 - - + +
317D ILE* 4.0 6.5 - - + -
351D GLY 3.7 5.2 - - - +
352D PHE* 3.9 2.5 - - - -
353D SER* 3.2 55.4 - - - +
383D TRP* 4.5 18.2 - - + -
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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