Contacts of the helix formed by residues 298 - 311 (chain W) in PDB entry 4UJ3
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 ASP 298 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296W GLU 3.4 4.9 + - - +
297W ALA* 1.3 69.0 - - - +
299W LEU* 1.3 64.4 + - - +
300W SER* 3.1 14.9 + - - -
301W LEU* 2.7 53.7 + - + +
302W TYR* 2.9 20.7 + - - +
438W PHE* 4.2 4.1 - - - -
442W MET* 4.8 4.8 - - + +
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Residues in contact with LEU 299 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297W ALA* 3.2 14.8 + - + +
298W ASP* 1.3 71.1 + - - +
300W SER* 1.3 58.3 + - - +
302W TYR* 3.4 13.9 - - + +
303W ASN* 2.8 46.5 + - - +
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Residues in contact with SER 300 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298W ASP* 3.1 15.8 + - - -
299W LEU* 1.3 80.5 - - - +
301W LEU* 1.3 61.4 + - - +
303W ASN* 4.3 4.6 - - - +
304W GLU* 3.3 22.4 + - - +
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Residues in contact with LEU 301 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298W ASP* 2.7 31.1 + - + +
300W SER* 1.3 75.4 - - - +
302W TYR* 1.3 57.2 + - - +
304W GLU* 3.5 13.2 + - - +
305W PHE* 2.9 29.6 + - - +
320W PHE* 5.5 1.2 - - - -
323W LYS* 3.8 30.1 - - + -
438W PHE* 3.7 4.5 - - + -
442W MET* 3.4 33.7 - - + -
445W ARG* 4.0 21.8 - - - +
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Residues in contact with TYR 302 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297W ALA* 4.7 8.5 - - + -
298W ASP 2.9 12.9 + - - +
299W LEU* 3.0 18.6 + - + +
301W LEU* 1.3 75.3 - - - +
303W ASN* 1.3 73.7 + - - +
305W PHE* 3.2 3.5 + + - +
306W ARG* 2.8 49.0 + - + +
434W VAL* 3.9 19.9 - - + +
435W ASP* 2.6 30.2 + - - -
438W PHE* 3.3 50.2 - + + -
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Residues in contact with ASN 303 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299W LEU* 2.8 31.1 + - - +
300W SER* 4.3 3.7 - - - +
302W TYR* 1.3 87.3 - - - +
304W GLU* 1.3 64.0 + - - +
306W ARG* 3.2 9.5 + - - +
307W LEU* 2.9 36.8 + - + +
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Residues in contact with GLU 304 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300W SER 3.3 16.9 + - - +
301W LEU* 3.6 14.7 - - - +
302W TYR 3.2 0.2 - - - -
303W ASN* 1.3 79.4 - - - +
305W PHE* 1.3 61.7 + - - +
307W LEU* 3.5 9.9 + - - +
308W TRP* 3.2 21.3 + - - +
319W PRO* 3.5 21.7 - - + +
320W PHE* 4.0 30.9 - - + +
323W LYS* 3.0 41.7 + - - +
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Residues in contact with PHE 305 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301W LEU 2.9 18.6 + - - +
302W TYR* 3.6 4.3 - + - +
304W GLU* 1.3 75.7 - - - +
306W ARG* 1.3 70.5 + - + +
308W TRP* 2.9 12.8 + + - +
309W LYS* 2.9 36.7 + - + -
320W PHE* 3.6 36.7 - + + -
424W ILE* 4.3 10.1 - - + -
434W VAL* 4.1 12.8 - - + -
437W MET* 3.8 29.8 - - + -
438W PHE* 3.6 44.0 - + + -
441W VAL* 3.7 21.8 - - + -
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Residues in contact with ARG 306 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302W TYR* 2.8 39.6 + - + +
303W ASN* 3.2 11.0 + - - +
305W PHE* 1.3 84.8 - - + +
307W LEU* 1.3 65.8 + - + +
309W LYS* 3.6 7.4 + - + +
310W ASP* 3.4 33.1 + - - +
434W VAL* 3.3 46.1 - - + +
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Residues in contact with LEU 307 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303W ASN* 2.9 27.8 + - + +
304W GLU* 3.7 7.9 - - - +
305W PHE 3.0 0.2 - - - -
306W ARG* 1.3 80.7 - - + +
308W TRP* 1.3 66.6 + - - +
310W ASP* 3.1 21.6 + - + +
311W GLU* 3.3 11.3 + - - +
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Residues in contact with TRP 308 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304W GLU 3.2 9.4 + - - +
305W PHE* 2.9 12.8 + + - +
307W LEU* 1.3 79.6 - - - +
309W LYS* 1.3 62.8 + - - +
311W GLU 3.1 5.7 - - - +
312W PRO* 2.9 41.0 - - + +
313W THR* 2.9 49.3 + - + +
314W MET* 4.8 2.2 - - - -
318W CYS* 3.9 15.1 - - + -
320W PHE* 3.3 47.5 - + + -
321W LEU* 4.2 1.9 - - + +
421W ILE* 3.5 55.6 - - + -
424W ILE* 3.8 27.8 - - + -
425W GLN* 5.1 0.4 - - + -
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Residues in contact with LYS 309 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305W PHE* 2.9 31.1 + - + +
306W ARG* 3.9 8.1 - - + +
307W LEU 3.2 0.2 - - - -
308W TRP* 1.3 87.1 - - + +
310W ASP* 1.3 71.3 + - - +
312W PRO* 3.2 20.5 - - - +
424W ILE* 4.6 9.1 - - + +
429W VAL 5.9 1.4 + - - -
434W VAL* 3.4 40.2 - - + -
437W MET* 4.3 27.7 - - + +
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Residues in contact with ASP 310 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306W ARG* 3.4 27.9 + - - +
307W LEU* 3.1 15.9 + - + +
309W LYS* 1.3 93.7 + - - +
311W GLU* 1.3 69.2 + - + +
312W PRO* 3.4 3.4 - - - +
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Residues in contact with GLU 311 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307W LEU 3.3 6.9 + - - +
308W TRP* 3.1 10.5 + - - +
310W ASP* 1.3 87.0 - - + +
312W PRO* 1.3 68.2 - - - +
313W THR* 3.6 8.8 + - - +
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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