Contacts of the strand formed by residues 301 - 305 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B TYR* 4.6 0.4 - - + -
274B HIS 3.4 23.1 - - - +
275B TYR* 3.8 19.7 - - + -
290B VAL* 3.6 2.3 - - - -
291B CYS* 2.8 45.9 + - + +
293B ASP 3.8 10.5 - - - +
299B ASN 3.7 2.2 - - - +
300B ARG* 1.3 85.7 - - - +
302B TRP* 1.3 59.3 + - - +
315B GLY 3.3 11.4 - - - +
316B TYR* 3.5 34.3 - - + +
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Residues in contact with TRP 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B TYR* 2.6 23.6 + - - -
288B THR* 5.5 0.9 - - + -
289B CYS 3.0 15.7 - - - +
290B VAL* 4.4 4.7 - - + -
301B PRO* 1.3 73.9 - - - +
303B VAL* 1.3 69.9 + - - +
304B SER* 3.5 26.0 - - - -
313B GLN* 3.6 26.9 - - + -
314B ILE* 3.6 20.2 - - - -
315B GLY* 2.9 33.1 + - - -
316B TYR 3.1 31.4 + - - +
317B ILE* 3.8 6.3 - - + -
383B TRP* 3.5 53.1 + + + +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B VAL* 5.8 4.9 - - + -
254B ILE* 4.1 8.7 - - + -
268B LEU* 3.8 26.9 - - + -
275B TYR* 3.0 44.2 - - + +
278B CYS* 5.5 1.3 - - - -
288B THR* 3.6 0.3 - - - -
289B CYS* 2.8 41.6 + - + +
291B CYS* 5.0 3.1 - - - -
302B TRP* 1.3 73.9 - - - +
304B SER* 1.3 65.3 + - - +
305B PHE* 4.0 20.3 - - + -
312B TYR* 4.4 1.6 - - + -
313B GLN 3.4 13.0 - - - +
314B ILE* 4.1 2.9 - - + -
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Residues in contact with SER 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLU* 5.5 4.3 - - - -
287B ILE 3.1 13.7 - - - -
288B THR* 4.0 14.6 - - - -
302B TRP* 3.5 21.3 - - - -
303B VAL* 1.3 74.7 - - - +
305B PHE* 1.3 68.7 + - - +
312B TYR* 3.1 2.6 - - - +
313B GLN* 3.0 42.4 + - - +
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Residues in contact with PHE 305 (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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238B PHE* 3.7 30.7 - + + -
239B THR 5.0 0.4 - - - -
240B VAL* 4.7 5.8 - - + -
254B ILE* 3.5 45.1 - - + -
280B CYS* 5.4 0.4 - - - -
286B GLU* 3.5 14.0 + - - +
287B ILE* 3.0 58.3 + - + +
289B CYS* 4.0 21.5 - - - -
303B VAL* 4.0 7.9 - - + -
304B SER* 1.3 83.8 - - - +
306B ASN* 1.3 74.8 + - - +
310B LEU* 4.3 7.0 - - + -
311B GLU 3.2 14.6 - - - +
312B TYR* 3.7 7.9 - - + +
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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