Contacts of the helix formed by residues 310 - 322 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134V ARG* 3.4 39.2 - - - +
135V LEU 2.9 10.5 + - - +
136V GLU* 3.8 15.5 - - - +
309V ILE* 1.3 83.2 - - - +
311V PHE* 1.3 83.1 + - + +
312V ARG* 3.0 62.8 + - - +
313V VAL* 3.1 12.3 + - - +
314V LEU* 3.5 2.3 + - - +
341V VAL* 3.4 22.9 - - + +
345V PHE* 4.1 9.4 - + - -
473V ASP* 2.9 23.3 + - - -
1482V EDO 4.5 0.2 - - - -
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Residues in contact with PHE 311 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269V TYR* 4.1 17.5 - - - -
295V ARG* 3.4 36.1 - - + -
298V HIS* 4.0 3.1 - - + -
302V ASP* 3.3 32.3 - - - +
310V HIS* 1.3 79.0 + - + +
312V ARG* 1.3 56.7 + - - +
314V LEU* 3.0 13.1 + - + -
315V ALA* 2.8 35.4 + - + -
326V LEU* 3.8 17.3 - - + -
327V HIS 3.4 23.3 - - - -
328V SER* 4.6 0.4 - - - -
345V PHE* 3.6 39.5 - + - -
349V MET* 4.8 1.3 - - - -
1482V EDO 3.5 16.6 - - - -
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Residues in contact with ARG 312 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136V GLU* 2.8 64.5 + - - +
137V ASP* 4.0 17.0 - - - +
310V HIS* 3.0 44.7 + - - +
311V PHE* 1.3 75.4 - - - +
313V VAL* 1.3 59.6 + - - +
315V ALA* 3.5 3.4 + - - +
316V LYS* 3.0 32.5 + - - +
341V VAL* 4.4 5.3 + - - +
344V GLY 6.2 0.2 - - - -
345V PHE* 3.7 30.2 - - + +
348V LEU* 4.1 16.8 - - + +
360V ARG 4.5 3.8 + - - -
361V GLY* 2.8 44.7 + - - -
363V TYR* 3.9 3.4 - - - -
475V LEU* 4.1 11.7 - - - +
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Residues in contact with VAL 313 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117V PHE* 4.1 11.4 - - + -
135V LEU* 3.8 25.4 - - + +
136V GLU 3.6 10.3 - - - +
137V ASP* 3.5 39.5 - - - +
138V LEU* 3.8 20.4 - - + +
309V ILE* 3.6 22.9 - - + -
310V HIS 3.1 2.5 + - - +
312V ARG* 1.3 74.0 - - + +
314V LEU* 1.3 59.8 + - - +
315V ALA 3.2 0.2 - - - -
316V LYS* 3.3 7.9 + - - +
317V ALA* 2.8 28.8 + - - +
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Residues in contact with LEU 314 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297O MET* 5.8 0.7 - - + -
117V PHE* 4.0 25.4 - - + -
269V TYR* 2.9 27.7 + - + +
270V LEU* 4.4 16.4 - - + -
274V PHE* 5.4 0.7 - - + -
298V HIS* 4.0 19.7 - - + +
301V ILE* 4.1 25.6 - - + -
302V ASP* 4.0 25.1 - - + +
309V ILE* 4.0 17.3 - - + -
310V HIS 4.0 8.1 - - - +
311V PHE* 3.0 11.3 + - + +
313V VAL* 1.3 75.2 - - - +
315V ALA* 1.3 57.9 + - - +
317V ALA* 3.6 6.1 + - - +
318V LEU* 3.0 19.9 + - - +
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Residues in contact with ALA 315 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311V PHE* 2.8 29.5 + - + +
312V ARG* 3.7 9.2 - - - +
313V VAL 3.2 0.2 - - - -
314V LEU* 1.3 71.6 - - - +
316V LYS* 1.3 60.5 + - - +
318V LEU* 3.3 3.1 + - - +
319V ARG* 2.9 28.2 + - - +
326V LEU* 3.8 27.4 - - + +
345V PHE* 5.0 4.0 - - + +
348V LEU* 6.1 1.8 - - + -
349V MET* 3.9 23.2 - - + +
374V VAL* 5.8 0.2 - - - +
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Residues in contact with LYS 316 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116V MET* 6.5 0.2 - - + -
137V ASP* 3.2 22.8 + - - +
138V LEU* 2.6 35.4 + - + +
139V ARG* 4.6 0.6 - - - +
140V ILE* 4.4 8.7 - - + -
312V ARG 3.0 21.1 + - - +
313V VAL* 3.3 7.2 + - + +
315V ALA* 1.3 74.6 - - - +
317V ALA* 1.3 63.9 + - - +
319V ARG* 3.2 3.3 + - - +
320V MET* 3.0 33.5 + - - +
348V LEU* 3.9 35.1 - - + +
364V PHE* 4.8 3.4 + - - +
366V GLN* 2.8 31.7 + - - +
368V TRP* 3.7 25.5 - - + -
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Residues in contact with ALA 317 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113V VAL* 3.5 15.8 - - + +
116V MET* 4.9 3.3 - - + +
117V PHE* 3.6 28.0 - - + -
274V PHE* 3.7 18.6 - - + -
313V VAL 2.8 17.8 + - - +
314V LEU 3.6 5.6 - - - +
316V LYS* 1.3 74.7 - - - +
318V LEU* 1.3 58.6 + - - +
320V MET* 3.3 9.5 + - - -
321V SER* 2.8 26.9 + - - -
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Residues in contact with LEU 318 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269V TYR* 3.6 31.6 - - + +
277V ASN* 3.6 20.6 - - - +
293V ILE* 3.7 34.3 - - + -
314V LEU 3.0 18.4 + - - +
315V ALA 3.6 4.3 - - - +
316V LYS 3.2 0.2 - - - -
317V ALA* 1.3 74.1 - - - +
319V ARG* 1.3 58.8 + - - +
321V SER* 4.4 3.1 - - - +
322V GLY* 2.7 37.3 + - - +
323V GLY* 4.0 11.7 - - - +
326V LEU* 4.0 28.3 - - + -
374V VAL* 4.4 9.2 - - + -
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Residues in contact with ARG 319 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151V HYP 2.8 38.3 + - - +
315V ALA 2.9 13.5 + - - +
316V LYS* 3.5 9.0 - - - +
318V LEU* 1.3 76.9 - - - +
320V MET* 1.3 60.3 + - - +
322V GLY 3.7 0.7 + - - -
348V LEU 2.8 29.8 + - - -
349V MET* 3.1 29.2 + - + +
350V ARG 4.0 0.4 + - - -
351V ASP 2.8 32.1 + - - -
352V ASP* 4.6 1.2 - - - +
368V TRP* 3.2 36.4 - - + +
371V MET* 2.8 37.5 + - - +
372V PRO 3.0 18.4 + - - +
373V GLY* 3.6 5.0 - - - +
374V VAL* 3.7 17.0 - - + -
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Residues in contact with MET 320 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113V VAL* 3.7 7.4 - - + -
116V MET* 3.9 30.1 - - + -
140V ILE* 3.7 41.3 - - + -
144V TYR* 4.0 1.6 - - + -
145V VAL* 5.7 0.9 - - + -
148V PHE* 3.4 53.9 - - + +
149V VAL 5.0 0.2 + - - -
150V GLY* 3.6 14.4 + - - -
278V THR* 5.6 0.3 - - - +
316V LYS 3.0 23.9 + - - +
317V ALA* 3.6 6.1 - - - +
319V ARG* 1.3 74.7 - - - +
321V SER* 1.3 63.6 + - - +
322V GLY 3.5 0.2 + - - -
368V TRP* 3.8 16.8 - - + -
371V MET* 4.0 12.3 - - + -
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Residues in contact with SER 321 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113V VAL* 3.7 8.2 - - - +
148V PHE* 5.0 0.4 - - - -
149V VAL* 6.1 0.3 - - - +
150V GLY 4.3 2.9 + - - +
274V PHE* 3.7 20.5 + - - -
277V ASN* 3.0 21.4 + - - +
278V THR* 2.8 42.6 + - - +
281V ALA* 3.6 14.0 - - - +
282V ILE* 6.0 0.2 - - - +
317V ALA 2.8 20.2 + - - -
318V LEU* 3.9 3.8 - - - -
320V MET* 1.3 74.4 - - - +
322V GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 322 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150V GLY 3.6 24.0 - - - -
151V HYP 3.8 1.8 - - - -
152V PRO* 4.1 0.7 - - - -
277V ASN* 3.0 21.8 - - - +
281V ALA* 3.7 10.8 - - - +
291V LEU* 3.8 9.7 - - - +
293V ILE* 3.9 0.3 - - - +
318V LEU* 2.7 21.3 + - - +
320V MET 3.3 1.6 - - - -
321V SER* 1.3 74.8 - - - +
323V GLY* 1.3 58.8 + - - -
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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