Contacts of the helix formed by residues 310 - 322 (chain O) in PDB entry 1UW9
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 HIS 310 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O ARG* 3.4 39.7 - - - +
135O LEU 2.9 10.4 + - - +
136O GLU* 3.8 16.4 - - - +
302O ASP* 4.3 0.4 - - - -
309O ILE* 1.3 74.8 - - - +
311O PHE* 1.3 80.5 + - + +
312O ARG* 3.0 63.5 + - - +
313O VAL* 3.1 18.5 + - - +
314O LEU* 3.6 3.5 + - - +
341O VAL* 3.4 22.7 - - + +
345O PHE* 4.1 9.2 - + - -
473O ASP* 2.9 23.7 + - - -
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Residues in contact with PHE 311 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269O TYR* 4.1 17.5 - - - -
295O ARG* 3.5 35.4 - - + -
298O HIS* 3.9 3.6 - - + -
302O ASP* 3.2 32.9 - - - +
310O HIS* 1.3 79.9 + - + +
312O ARG* 1.3 57.5 + - - +
314O LEU* 2.9 13.6 + - + -
315O ALA* 2.8 37.9 + - + -
326O LEU* 3.9 17.5 - - + -
327O HIS 3.4 22.9 - - - -
328O SER* 4.6 0.4 - - - -
345O PHE* 3.7 37.2 - + - -
349O MET* 4.7 1.1 - - - -
1483O EDO 3.6 15.9 - - - -
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Residues in contact with ARG 312 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136O GLU* 2.8 63.0 + - - +
137O ASP* 4.0 18.8 - - - +
310O HIS* 3.0 43.9 + - - +
311O PHE* 1.3 76.2 - - - +
313O VAL* 1.3 59.2 + - - +
315O ALA* 3.6 2.9 - - - +
316O LYS* 3.0 33.6 + - - +
341O VAL* 4.4 5.5 + - - +
345O PHE* 3.7 30.2 - - + +
348O LEU* 4.0 16.2 - - + +
360O ARG 4.4 4.0 + - - -
361O GLY* 2.9 45.7 + - - -
363O TYR* 4.0 4.2 - - - -
475O LEU* 4.1 11.5 - - - +
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Residues in contact with VAL 313 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O PHE* 4.2 11.0 - - + -
135O LEU* 3.8 24.0 - - + +
136O GLU 3.5 10.1 - - - +
137O ASP* 3.5 38.8 - - - +
138O LEU* 3.8 20.3 - - + +
309O ILE* 3.5 17.5 - - + -
310O HIS 3.1 10.2 + - - +
312O ARG* 1.3 76.0 - - + +
314O LEU* 1.3 60.1 + - - +
316O LYS* 3.4 8.4 + - + +
317O ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 314 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O PHE* 4.0 22.0 - - + -
269O TYR* 2.9 30.0 + - - +
270O LEU* 4.4 16.2 - - + -
274O PHE* 5.4 0.2 - - + -
298O HIS* 4.1 27.8 - - + +
301O ILE* 4.1 25.8 - - + -
302O ASP* 4.1 16.2 - - + +
309O ILE* 4.0 20.4 - - + -
310O HIS 3.6 8.3 + - - +
311O PHE* 2.9 11.5 + - + +
313O VAL* 1.3 77.1 - - - +
315O ALA* 1.3 56.5 + - - +
317O ALA* 3.6 4.5 + - - +
318O LEU* 3.1 19.9 + - - +
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Residues in contact with ALA 315 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311O PHE* 2.8 26.6 + - + +
312O ARG* 3.6 9.0 - - - +
314O LEU* 1.3 75.2 - - - +
316O LYS* 1.3 58.8 + - - +
318O LEU* 3.2 3.5 + - - +
319O ARG* 2.9 29.0 + - - +
326O LEU* 3.8 26.2 - - + +
345O PHE* 5.0 4.0 - - + +
348O LEU* 6.1 2.2 - - + -
349O MET* 3.9 21.8 - - + +
374O VAL* 5.8 0.2 - - - +
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Residues in contact with LYS 316 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137O ASP* 3.2 22.1 + - - +
138O LEU* 2.5 35.4 + - + +
139O ARG* 4.6 1.0 - - - +
140O ILE* 4.4 8.1 - - + -
312O ARG 3.0 19.5 + - - +
313O VAL* 3.4 7.4 + - + +
315O ALA* 1.3 74.5 - - - +
317O ALA* 1.3 63.4 + - - +
319O ARG* 3.1 4.3 + - - +
320O MET* 3.0 32.3 + - - +
348O LEU* 3.8 35.7 - - + +
364O PHE* 4.9 3.4 + - - +
366O GLN* 2.8 32.4 + - - +
368O TRP* 3.6 26.1 - - + -
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Residues in contact with ALA 317 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O VAL* 3.4 11.7 - - + +
116O MET* 4.9 2.4 - - + +
117O PHE* 3.7 28.5 - - + -
274O PHE* 3.7 21.3 - - + -
313O VAL 2.9 17.4 + - - +
314O LEU 3.7 3.1 - - - +
315O ALA 3.3 0.2 - - - -
316O LYS* 1.3 75.7 - - - +
318O LEU* 1.3 57.2 + - - +
320O MET* 3.3 11.2 + - - -
321O SER* 2.9 29.6 + - - -
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Residues in contact with LEU 318 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269O TYR* 3.6 36.9 - - + -
277O ASN* 3.6 20.4 - - - +
293O ILE* 3.7 35.0 - - + -
314O LEU 3.1 10.1 + - - +
315O ALA 3.2 7.6 + - - +
317O ALA* 1.3 72.1 - - - +
319O ARG* 1.3 61.4 + - - +
321O SER* 4.4 2.7 - - - +
322O GLY* 2.7 34.7 + - - +
323O GLY* 4.0 11.7 - - - +
326O LEU* 3.9 32.1 - - + -
374O VAL* 4.3 9.2 - - + -
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Residues in contact with ARG 319 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151O HYP 2.8 38.0 + - - +
315O ALA 2.9 14.2 + - - +
316O LYS* 3.1 9.2 + - - +
318O LEU* 1.3 76.6 - - - +
320O MET* 1.3 60.4 + - - +
322O GLY 3.8 0.3 + - - -
348O LEU 2.8 35.5 + - - -
349O MET* 3.0 28.3 + - + +
350O ARG 3.9 0.4 + - - -
351O ASP 2.8 31.9 + - - -
352O ASP* 4.7 0.8 - - - +
368O TRP* 3.2 30.5 - - + +
371O MET* 2.8 38.2 + - - +
372O PRO 2.9 20.1 + - - +
373O GLY* 3.5 5.2 - - - +
374O VAL* 3.7 17.3 - - + -
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Residues in contact with MET 320 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O VAL* 3.7 7.6 - - + -
116O MET* 3.8 30.3 - - + -
140O ILE* 3.7 41.1 - - + -
144O TYR* 4.0 1.1 - - + -
145O VAL* 5.7 1.1 - - + -
148O PHE* 3.5 54.0 - - + +
149O VAL 5.0 0.2 + - - -
150O GLY* 3.5 17.7 + - - -
278O THR* 5.6 0.3 - - - +
316O LYS 3.0 19.8 + - - +
317O ALA* 3.6 6.3 - - - +
319O ARG* 1.3 74.6 - - - +
321O SER* 1.3 65.0 + - - +
368O TRP* 3.9 16.4 - - + -
371O MET* 4.1 12.6 - - + -
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Residues in contact with SER 321 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113O VAL* 3.7 12.9 - - - +
148O PHE* 5.0 0.9 - - - -
149O VAL* 6.1 0.2 - - - +
150O GLY 4.2 3.5 + - - +
274O PHE* 3.7 17.6 + - - -
277O ASN* 3.0 19.9 + - - +
278O THR* 2.8 43.8 + - - +
281O ALA* 3.6 13.5 - - - +
282O ILE* 6.0 0.2 - - - +
317O ALA 2.9 19.4 + - - -
318O LEU* 3.9 3.6 - - - -
320O MET* 1.3 74.1 - - - +
322O GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 322 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150O GLY 3.5 25.1 - - - -
151O HYP 3.8 1.6 - - - -
152O PRO* 4.1 0.9 - - - -
277O ASN* 3.1 19.1 - - - +
281O ALA* 3.7 10.3 - - - +
291O LEU* 3.7 10.9 - - - +
293O ILE* 3.9 0.3 - - - +
318O LEU* 2.7 21.0 + - - +
320O MET 3.3 0.8 - - - -
321O SER* 1.3 74.9 - - - +
323O GLY* 1.3 57.4 + - - -
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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