Contacts of the strand formed by residues 301 - 305 (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 PRO 301 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D TYR* 4.6 0.9 - - + -
274D HIS 3.5 20.9 - - - +
275D TYR* 3.8 16.2 - - + -
290D VAL* 3.5 4.3 - - - +
291D CYS* 2.8 54.7 + - + +
293D ASP* 3.8 11.7 - - + +
300D ARG* 1.3 87.2 - - - +
302D TRP* 1.3 62.5 + - - +
315D GLY 3.3 9.4 - - - +
316D TYR* 3.7 29.2 - - + +
317D ILE* 5.5 0.2 - - - -
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Residues in contact with TRP 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D TYR* 2.8 17.2 + - - -
288D THR* 5.5 1.3 - - + -
289D CYS 2.9 17.0 - - - +
290D VAL* 4.4 3.6 - - + -
301D PRO* 1.3 75.5 - - - +
303D VAL* 1.3 68.2 + - - +
304D SER* 3.5 17.7 - - - -
313D GLN* 3.3 36.3 - - + -
314D ILE* 3.4 13.7 - - - -
315D GLY* 2.8 50.5 + - - -
316D TYR* 3.4 20.1 + - - +
317D ILE* 3.8 8.0 - - + +
383D TRP* 3.5 54.2 + + + +
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Residues in contact with VAL 303 (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* 5.3 5.6 - - + -
254D ILE* 4.2 17.0 - - + -
268D LEU* 3.7 27.6 - - + -
275D TYR* 3.1 33.2 - - + -
278D CYS* 4.8 2.0 - - - -
287D ILE 4.0 0.2 - - - +
288D THR* 3.5 0.9 - - - +
289D CYS* 2.6 53.1 + - + +
291D CYS* 4.3 1.6 - - - -
302D TRP* 1.3 73.0 - - - +
304D SER* 1.3 61.5 + - - +
305D PHE* 4.4 7.9 - - + -
312D TYR* 4.5 3.8 - - + -
313D GLN 3.4 11.4 - - - +
314D ILE* 3.8 8.5 - - + -
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Residues in contact with SER 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D GLU* 5.3 5.7 + - - -
287D ILE 2.9 13.5 - - - -
288D THR* 3.9 14.6 - - - -
302D TRP* 3.5 22.1 - - - -
303D VAL* 1.3 75.2 - - - +
305D PHE* 1.3 65.3 + - - +
312D TYR* 3.4 1.0 - - - +
313D GLN* 3.0 40.8 + - - +
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Residues in contact with PHE 305 (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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238D PHE* 3.8 28.5 - + + -
239D THR 5.2 0.4 - - - -
240D VAL* 4.8 3.8 - - + -
254D ILE* 3.2 52.0 - - + -
280D CYS* 5.7 0.4 - - - -
286D GLU* 3.4 11.6 + - - +
287D ILE* 3.0 63.2 + - + +
289D CYS* 4.2 16.2 - - - -
303D VAL* 4.4 4.3 - - + -
304D SER* 1.3 83.9 - - - +
306D ASN* 1.3 73.9 + - - +
310D LEU* 4.4 7.4 - - + -
311D GLU 3.2 16.2 - - - +
312D TYR* 3.6 9.2 - - + -
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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
------------------------------------------------------------
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