Contacts of the helix formed by residues 307 - 324 (chain A) in PDB entry 2UYC
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 VAL 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ALA* 3.8 10.1 - - + -
159A ILE* 3.7 37.0 - - + -
161A GLN* 4.8 0.9 - - + -
163A ASN* 3.6 37.3 + - + +
167A TYR* 5.1 4.1 + - - +
282A VAL 4.7 3.1 - - - +
283A MET* 3.2 21.3 - - - +
306A VAL* 1.3 73.0 - - - +
308A ILE* 1.3 67.6 + - - +
309A ASN 4.2 2.9 - - - +
310A VAL* 3.2 33.2 + - + +
311A LEU* 3.3 11.8 + - - +
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Residues in contact with ILE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.6 26.0 - - + -
23A GLY* 3.5 35.4 - - - +
26A LEU* 4.1 9.2 - - + -
27A ALA* 4.2 15.9 - - + +
283A MET 3.0 14.1 + - - +
284A GLY 3.6 21.8 - - - +
285A TYR* 3.7 24.7 - - + -
306A VAL* 4.1 4.3 - - + +
307A VAL* 1.3 69.7 - - - +
309A ASN* 1.3 57.2 + - - +
311A LEU* 3.0 9.3 + - - +
312A GLN* 2.8 36.0 + - + +
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Residues in contact with ASN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.2 28.2 + - - +
2A ILE* 3.6 26.2 - - + +
157A TYR 4.0 14.1 + - - +
158A GLY* 5.1 2.4 + - - -
159A ILE* 3.5 30.9 - - + +
284A GLY* 3.4 15.6 - - - -
307A VAL* 3.4 1.0 - - + -
308A ILE* 1.3 72.7 - - - +
310A VAL* 1.3 62.3 + - - +
312A GLN* 3.2 12.6 + - - +
313A TYR* 3.0 34.7 + - + -
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 4.1 20.9 - - + +
154A ALA* 4.0 22.4 - - + +
157A TYR* 4.1 18.8 - - + +
159A ILE* 5.8 0.2 - - + -
167A TYR* 3.6 37.2 - - + +
183A PRO* 6.0 0.4 - - + -
307A VAL* 3.2 29.7 + - + +
309A ASN* 1.3 75.8 - - + +
311A LEU* 1.3 63.3 + - - +
313A TYR* 3.3 10.2 + - - +
314A ILE* 3.1 24.7 + - + +
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 4.0 3.1 - - - +
24A PHE* 3.8 42.0 - - + +
27A ALA* 3.5 11.8 - - + +
117A PHE* 3.7 25.9 - - + -
167A TYR* 3.6 29.8 - - + +
306A VAL* 3.3 35.4 - - + -
307A VAL 3.3 10.9 + - - +
308A ILE* 3.0 7.4 + - - +
310A VAL* 1.3 77.3 - - - +
312A GLN* 1.3 57.6 + - - +
314A ILE* 3.7 0.9 - - - +
315A ALA* 2.8 32.2 + - - +
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Residues in contact with GLN 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.3 18.8 - - - +
2A ILE* 2.8 62.5 + - + +
4A ILE* 3.9 8.6 - - + +
27A ALA* 4.0 17.0 - - - -
30A SER* 3.1 31.0 + - - +
31A CYS* 4.0 3.2 - - - -
308A ILE* 2.8 15.4 + - + +
309A ASN* 3.2 14.8 + - - +
311A LEU* 1.3 76.8 - - - +
313A TYR* 1.3 58.0 + - - +
315A ALA* 3.3 4.1 + - - +
316A TYR* 2.9 30.5 + - - +
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Residues in contact with TYR 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ILE* 3.6 44.0 - - + +
4A ILE* 5.8 1.3 - - + -
157A TYR* 3.6 38.2 + + + -
183A PRO* 3.4 24.0 - - + -
186A PHE* 3.3 31.0 - + - -
309A ASN* 3.0 25.9 + - + -
310A VAL* 3.3 3.8 + - - +
312A GLN* 1.3 76.5 - - - +
314A ILE* 1.3 62.8 + - - +
316A TYR* 3.5 6.4 + - + +
317A ASN* 3.1 30.2 + - - +
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Residues in contact with ILE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 3.3 27.8 - - + -
152A LEU* 4.1 6.1 - - + -
167A TYR* 3.5 45.8 - - + -
169A ILE* 3.6 22.4 - - + -
180A PHE* 4.3 5.2 - - + -
182A PHE* 4.9 2.7 - - + -
183A PRO* 3.9 23.3 - - + -
310A VAL* 3.1 22.4 + - + +
311A LEU 3.7 0.4 - - - +
313A TYR* 1.3 75.4 - - - +
315A ALA* 1.3 58.4 + - - +
317A ASN* 3.0 6.2 + - - +
318A ILE* 2.8 31.6 + - + +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.9 16.7 - - + +
27A ALA 4.5 2.5 - - - +
28A LEU* 4.1 24.9 - - + -
31A CYS* 4.1 15.0 - - - -
117A PHE* 4.5 2.0 - - + -
311A LEU 2.8 22.6 + - - +
312A GLN* 3.7 5.2 - - - +
314A ILE* 1.3 74.0 - - - +
316A TYR* 1.3 61.6 + - - +
318A ILE* 3.2 14.4 + - + +
319A GLY* 3.0 19.6 + - - -
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Residues in contact with TYR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.9 20.4 - - + -
6A ASP* 3.3 45.3 + - - +
8A GLN* 3.5 24.8 + - + +
31A CYS* 3.9 8.7 - - - -
312A GLN 2.9 16.8 + - - +
313A TYR* 3.6 9.9 - - + +
315A ALA* 1.3 76.0 - - - +
317A ASN* 1.3 67.8 + - - +
319A GLY 3.4 1.0 + - - -
320A SER* 2.9 47.2 + - - -
1336A GOL 3.6 20.6 - - - -
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Residues in contact with ASN 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A PHE* 4.0 9.1 - - + -
181A GLN* 2.7 46.0 + - + +
182A PHE 3.8 0.4 - - - -
183A PRO* 3.7 21.6 - - - +
313A TYR* 3.1 14.4 + - - +
314A ILE* 3.0 10.6 + - - +
316A TYR* 1.3 89.1 - - - +
318A ILE* 1.3 64.6 + - - +
320A SER* 3.6 9.1 + - - -
321A SER* 3.1 25.5 + - - -
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.7 1.3 - - + -
74A ILE* 4.5 12.6 - - + -
115A VAL* 3.9 23.3 - - + -
117A PHE* 3.9 30.3 - - + -
169A ILE* 3.7 31.2 - - + -
171A PHE* 4.1 5.1 - - + -
180A PHE* 3.7 11.9 - - + -
314A ILE* 2.8 24.1 + - + +
315A ALA* 3.2 10.7 + - - +
317A ASN* 1.3 76.0 - - - +
319A GLY* 1.3 63.9 + - - +
321A SER* 3.2 4.2 + - - -
322A LEU* 3.0 40.1 + - + +
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Residues in contact with GLY 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLN* 3.8 11.0 - - - -
9A LEU* 3.5 22.7 - - - -
315A ALA 3.0 10.5 + - - -
316A TYR 3.8 3.1 - - - -
318A ILE* 1.3 76.1 - - - +
320A SER* 1.3 64.3 + - - +
322A LEU* 3.2 5.6 + - - -
323A ASN* 2.9 35.7 + - - +
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Residues in contact with SER 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN* 3.7 13.5 + - - -
179A ASN* 5.0 0.6 + - - -
316A TYR* 2.9 45.0 + - - -
317A ASN* 3.6 12.2 + - - -
318A ILE 3.3 0.2 - - - -
319A GLY* 1.3 75.6 - - - +
321A SER* 1.3 61.5 + - - +
323A ASN* 3.5 2.3 + - - +
324A PHE* 3.3 21.7 + - - +
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Residues in contact with SER 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PHE* 4.4 5.2 - - - -
177A ILE* 3.7 28.1 - - - +
179A ASN* 2.7 34.1 + - - +
180A PHE* 3.2 23.0 - - - -
317A ASN 3.1 12.0 + - - -
318A ILE 3.6 7.0 - - - -
320A SER* 1.3 76.2 - - - +
322A LEU* 1.3 63.9 + - - +
323A ASN 3.1 0.9 + - - -
324A PHE* 3.4 16.6 + - - +
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.8 28.9 - - + -
73A ASP* 6.4 0.2 - - + -
74A ILE* 4.7 3.6 - - + -
114A LYS* 4.7 12.3 - - + -
115A VAL* 4.0 15.3 - - + -
171A PHE* 3.8 24.7 - - + -
175A LEU* 4.2 18.8 - - + -
177A ILE* 4.2 9.2 - - + +
318A ILE* 3.0 36.0 + - + +
319A GLY* 3.2 5.4 + - - +
321A SER* 1.3 75.9 - - - +
323A ASN* 1.3 64.7 + - - +
325A LYS* 2.8 30.7 - - - +
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Residues in contact with ASN 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLN* 2.7 50.8 + - - +
12A LEU* 5.7 2.3 - - - +
319A GLY* 2.9 16.7 + - - +
320A SER 4.0 3.6 - - - +
321A SER 3.1 0.2 - - - -
322A LEU* 1.3 83.3 - - - +
324A PHE* 1.3 59.4 + - - +
325A LYS* 3.0 20.8 + - - +
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Residues in contact with PHE 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ILE* 5.8 1.0 - - - +
179A ASN* 3.3 32.1 - - - +
320A SER 3.3 13.2 + - - +
321A SER 3.4 9.4 + - - +
323A ASN* 1.3 74.8 - - - +
325A LYS* 1.3 59.9 + - - +
326A PRO* 3.4 33.4 - - + +
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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
------------------------------------------------------------
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