Contacts of the helix formed by residues 305 - 317 (chain A) in PDB entry 3QV2
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 SER 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PRO* 3.5 26.2 - - - +
163A ASN* 6.0 0.2 - - - -
165A ARG* 4.5 11.5 - - - +
167A ARG* 6.4 0.4 - - - +
169A TYR* 4.6 8.2 + - - -
277A ILE 5.3 1.3 + - - -
278A HIS* 3.7 10.0 - - - +
304A VAL* 1.3 75.3 - - - +
306A CYS* 1.3 64.2 + - - +
307A PHE* 3.8 11.4 + - - +
308A VAL* 3.0 33.2 + - - +
309A ILE* 3.1 15.5 + - - +
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Residues in contact with CYS 306 (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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17A GLY* 3.6 22.9 - - - -
20A SER* 3.7 17.3 - - - -
21A SER* 3.1 16.6 + - - +
24A ARG* 3.8 9.5 - - - -
278A HIS 2.8 19.7 + - - +
279A GLY 3.5 16.4 - - - +
280A PHE* 3.9 25.1 - - - -
304A VAL* 3.6 2.2 + - - -
305A SER* 1.3 72.4 - - - +
307A PHE* 1.3 62.5 + - - +
310A ALA* 2.9 28.1 + - - +
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Residues in contact with PHE 307 (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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24A ARG* 3.5 32.1 - - - +
159A ILE* 3.9 7.9 - - + +
161A ILE* 3.8 44.0 - - + -
186A GLU* 4.1 20.3 - - + +
194A TYR* 4.4 11.2 - + - -
276A LYS 3.8 7.9 - - - -
277A ILE 3.5 22.2 - - - -
278A HIS 4.1 1.3 - - - -
279A GLY* 3.2 30.3 - - - -
305A SER* 3.0 7.6 - - - +
306A CYS* 1.3 79.5 - - - +
308A VAL* 1.3 63.6 + - - +
310A ALA* 3.5 13.5 + - - +
311A GLN* 3.6 13.0 + - - +
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A CYS* 3.6 29.8 - - - +
155A SER 4.2 3.4 - - - +
156A PRO* 3.6 34.3 - - + -
159A ILE* 3.8 16.8 - - + -
169A TYR* 3.7 22.0 - - + +
183A LEU* 5.8 3.0 - - + +
305A SER* 3.0 22.0 + - - +
307A PHE* 1.3 71.3 - - - +
309A ILE* 1.3 67.5 + - - +
311A GLN* 3.1 14.3 + - - +
312A LEU* 3.2 18.3 + - + +
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Residues in contact with ILE 309 (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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18A LEU* 3.8 17.0 - - + -
21A SER* 3.3 15.5 - - - +
122A PHE* 3.6 13.5 - - + -
124A GLU* 4.2 3.4 - - + -
169A TYR* 3.6 26.2 - - + +
304A VAL* 3.6 40.6 - - + -
305A SER 3.1 9.2 + - - +
308A VAL* 1.3 76.3 - - - +
310A ALA* 1.3 56.9 + - - +
312A LEU* 3.2 6.8 + - - -
313A MET* 2.8 60.2 + - + +
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Residues in contact with ALA 310 (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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21A SER* 3.5 25.3 - - - +
24A ARG* 3.9 15.9 - - + +
25A SER* 3.6 12.4 - - - -
306A CYS 2.9 20.6 + - - +
307A PHE 3.6 5.8 - - - +
309A ILE* 1.3 77.5 - - - +
311A GLN* 1.3 61.1 + - + +
313A MET* 3.8 1.2 - - - +
314A GLU* 3.1 33.7 + - - +
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Residues in contact with GLN 311 (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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159A ILE* 3.7 19.3 - - + +
182A GLN 4.2 7.7 - - - +
183A LEU* 3.4 18.2 - - + +
184A HIS* 2.8 57.9 + - + +
186A GLU* 3.3 23.6 + - - +
307A PHE 3.9 10.3 - - - +
308A VAL* 3.1 8.7 + - - +
310A ALA* 1.3 78.3 - - + +
312A LEU* 1.3 62.6 + - - +
314A GLU* 3.4 20.4 + - - +
315A TYR* 3.3 18.4 + - - +
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 3.8 15.3 - - + -
152A ILE* 3.9 11.9 - - + -
154A CYS* 4.4 1.3 - - - -
169A TYR* 3.3 51.1 - - + -
171A MET* 3.5 13.3 - - - +
181A ILE* 3.7 28.3 - - + -
182A GLN 5.8 0.2 - - - +
183A LEU* 4.0 21.8 - - + -
308A VAL* 3.2 22.4 + - + +
309A ILE 3.8 3.4 - - - +
311A GLN* 1.3 73.9 - - - +
313A MET* 1.3 60.6 + - - +
315A TYR* 3.2 7.4 + - - +
316A LEU* 2.9 22.3 + - - +
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Residues in contact with MET 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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18A LEU* 3.4 22.4 - - + +
21A SER* 4.1 0.9 - - - -
22A TYR* 3.7 33.0 - - - -
25A SER* 5.2 1.1 - - - +
27A ILE* 3.9 12.3 - - + -
76A PHE* 3.5 34.8 - - + -
122A PHE* 4.0 20.4 - - + -
309A ILE* 2.8 43.0 + - + +
310A ALA* 3.8 4.3 - - - +
312A LEU* 1.3 72.5 - - - +
314A GLU* 1.3 60.1 + - - +
315A TYR 3.0 1.8 - - - -
316A LEU* 3.1 6.5 + - - -
317A PHE* 2.9 39.8 + - + -
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Residues in contact with GLU 314 (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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25A SER* 3.4 18.8 - - - -
26A SER* 2.8 40.6 + - - +
27A ILE* 4.0 13.5 - - + -
184A HIS* 5.1 10.7 + - - -
310A ALA* 3.1 18.5 + - - +
311A GLN* 3.5 19.7 - - - +
312A LEU 3.3 0.2 - - - -
313A MET* 1.3 76.1 - - - +
315A TYR* 1.3 60.0 + - - +
317A PHE* 3.7 1.4 + - - +
318A ASP* 3.3 21.7 + - - +
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Residues in contact with TYR 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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150A LYS* 3.0 40.2 - - + +
171A MET* 3.7 19.1 - - - -
173A ARG* 3.4 2.4 + - - -
177A PHE* 3.4 29.0 - + - +
179A ASN* 3.0 30.1 + - + -
180A GLU 3.7 3.1 - - - -
181A ILE* 3.3 47.9 + - + -
182A GLN* 4.7 5.2 - - + +
311A GLN 3.3 8.7 + - - +
312A LEU* 3.2 9.6 + - - +
314A GLU* 1.3 76.9 - - - +
316A LEU* 1.3 66.4 + - - +
318A ASP* 3.0 36.8 + - - +
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Residues in contact with LEU 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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76A PHE* 4.7 1.3 - - + -
120A HIS* 3.2 31.7 - - + -
121A ILE 3.6 17.7 - - - +
122A PHE* 3.8 24.5 - - + -
171A MET* 3.9 12.6 - - + -
172A ALA 3.4 39.0 - - - +
173A ARG* 2.7 26.4 + - + -
177A PHE* 4.2 8.5 - - + -
312A LEU 2.9 14.1 + - - +
313A MET* 3.1 8.3 + - - +
315A TYR* 1.3 77.9 - - - +
317A PHE* 1.3 74.4 + - + +
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Residues in contact with PHE 317 (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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6A VAL* 4.1 26.5 - - + -
22A TYR* 4.4 2.9 - + - -
27A ILE* 3.5 32.9 - - + +
74A THR* 3.9 9.0 - - + -
76A PHE* 3.7 31.0 - + - -
120A HIS* 3.5 34.8 - + + -
313A MET* 2.9 30.0 + - + +
314A GLU 3.9 3.6 - - - +
316A LEU* 1.3 90.9 - - + +
318A ASP* 1.3 56.9 + - - +
319A ASP* 2.9 15.8 + - - -
320A LEU* 3.0 40.9 + - + +
321A LYS* 4.4 1.4 + - - +
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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
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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