Contacts of the helix formed by residues 237 - 255 (chain A) in PDB entry 3C6Q
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 ARG 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLY 4.6 0.2 - - - +
236A GLN* 1.3 76.1 - - - +
238A PRO* 1.3 64.6 - - - +
239A TYR* 3.2 4.5 - - + +
240A MET* 3.2 31.3 + - + +
241A MET* 3.3 20.2 + - - +
279A THR* 3.0 32.8 + - - +
280A GLY* 3.9 9.8 + - - +
281A VAL 3.2 29.7 + - - +
282A ASP* 3.1 40.6 + - - +
295A LYS* 4.5 8.3 - - - +
296A MET* 6.0 3.1 - - + -
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Residues in contact with PRO 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.2 48.0 - - + +
17A GLN* 3.8 21.1 - - + +
18A VAL* 3.4 27.2 - - + +
236A GLN* 3.1 12.1 - - + +
237A ARG* 1.3 87.3 - - - +
239A TYR* 1.3 68.7 + - + +
241A MET* 2.8 29.7 + - + +
242A GLY 3.4 3.8 + - - -
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Residues in contact with TYR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLN* 3.0 19.7 + - - +
20A GLN* 3.4 17.0 - - + -
21A GLY* 3.3 41.0 - - - -
24A ALA* 2.9 24.9 - - + +
237A ARG* 3.2 2.4 - - + -
238A PRO* 1.3 82.0 - - - +
240A MET* 1.3 81.3 + - + +
241A MET 3.0 1.4 + - - -
242A GLY 3.3 0.9 + - - -
243A TYR* 3.1 38.0 + + - +
296A MET* 6.3 0.7 - - + -
299A LEU* 3.9 49.9 + - + +
301A ILE* 4.3 22.9 - - + -
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Residues in contact with MET 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ARG* 3.2 33.1 + - + +
238A PRO 3.2 0.6 - - - -
239A TYR* 1.3 99.9 - - + +
241A MET* 1.3 60.5 + - - +
243A TYR* 3.9 12.1 - - + -
244A LEU* 3.1 63.0 + - + +
279A THR* 4.2 12.5 - - + +
299A LEU* 6.2 1.1 - - + -
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Residues in contact with MET 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.2 28.7 - - - +
18A VAL* 4.7 2.7 - - + -
88A LEU* 4.0 15.3 - - + -
89A ASP* 3.9 29.6 - - - +
101A ILE* 4.1 6.3 - - - +
102A GLY* 4.1 4.9 - - - -
103A THR* 3.4 30.3 - - - +
236A GLN* 4.5 1.1 - - - +
237A ARG 3.3 20.4 - - - +
238A PRO* 2.8 15.7 + - + +
240A MET* 1.3 76.6 - - - +
242A GLY* 1.3 57.9 + - - +
244A LEU* 3.8 0.3 - - - -
245A SER* 2.6 38.9 + - - -
279A THR* 3.9 25.1 - - + +
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Residues in contact with GLY 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.0 5.1 - - - +
22A VAL* 3.7 27.8 - - - +
88A LEU* 4.0 14.0 - - - +
238A PRO 3.4 4.2 + - - -
239A TYR 3.3 4.7 + - - -
241A MET* 1.3 76.5 - - - +
243A TYR* 1.3 66.3 + - - +
245A SER* 3.1 3.1 + - - -
246A VAL* 2.9 28.4 + - - +
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Residues in contact with TYR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 3.4 26.1 - - - +
24A ALA* 3.5 21.7 + - + -
25A ALA* 3.5 13.9 - - + +
28A ALA* 4.1 18.5 - - - +
29A LEU* 6.4 0.7 - - + -
239A TYR* 3.1 41.8 + + + +
240A MET* 3.7 17.0 - - + +
242A GLY* 1.3 77.1 - - - +
244A LEU* 1.3 70.0 + - + +
246A VAL* 3.2 3.8 + - - +
247A THR* 3.0 42.0 + - - -
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 3.9 14.1 - - + -
240A MET* 3.1 46.0 + - + +
241A MET 4.2 1.1 - - - +
243A TYR* 1.3 85.5 - - + +
245A SER* 1.3 60.7 + - - +
246A VAL 3.2 0.9 - - - -
247A THR* 4.1 13.5 - - + +
248A VAL* 2.8 39.2 + - + +
277A ILE* 4.3 26.0 - - + -
279A THR* 4.6 7.6 - - + -
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 5.7 0.2 - - - -
6A VAL* 5.4 1.8 - - - -
62A ALA* 3.8 23.1 - - - +
86A VAL* 4.2 5.3 - - - +
88A LEU* 3.4 23.4 - - - +
101A ILE* 3.8 15.6 - - - +
241A MET 2.6 23.5 + - - -
242A GLY* 3.4 9.2 - - - -
244A LEU* 1.3 78.6 - - - +
246A VAL* 1.3 61.5 + - - +
248A VAL* 4.4 0.2 - - - +
249A LEU* 3.2 33.3 + - - +
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.7 23.2 - - + +
6A VAL* 4.5 9.9 - - + -
22A VAL* 3.8 34.5 - - + +
25A ALA* 3.5 18.4 - - + -
26A GLY 4.4 0.7 - - - +
29A LEU* 4.5 3.1 - - + -
31A VAL* 4.0 18.8 - - + -
33A THR* 4.4 7.0 - - + -
242A GLY 2.9 18.3 + - - +
243A TYR 3.5 6.3 - - - +
244A LEU 3.2 0.2 - - - -
245A SER* 1.3 75.2 - - - +
247A THR* 1.3 56.3 + - - +
249A LEU* 3.0 4.7 + - - +
250A TYR* 2.8 33.1 + - - +
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Residues in contact with THR 247 (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 ALA* 4.4 0.7 - - - +
29A LEU* 3.8 27.1 - - + +
243A TYR* 3.0 32.9 + - - -
244A LEU* 3.9 14.5 - - + +
246A VAL* 1.3 77.1 - - - +
248A VAL* 1.3 67.1 + - + +
250A TYR* 2.9 4.8 + - + +
251A LEU* 2.9 41.2 + - + +
263A MET* 6.1 0.9 - - + -
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 4.1 15.3 - - + -
99A VAL* 4.5 9.4 - - + -
101A ILE* 4.2 5.4 - - + -
244A LEU* 2.8 27.8 + - + +
245A SER 4.4 0.9 - - - +
247A THR* 1.3 77.6 - - + +
249A LEU* 1.3 61.4 + - - +
251A LEU* 3.6 9.7 + - + -
252A MET* 3.3 47.1 + - + +
260A THR* 3.8 6.0 - - + +
263A MET* 6.1 0.7 - - + -
264A LEU* 4.3 16.2 - - + -
277A ILE* 4.0 26.2 - - + -
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Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.7 25.6 - - + -
60A GLY* 3.8 4.0 - - - -
61A ILE 3.4 35.9 - - - +
62A ALA* 3.7 10.5 - - + +
84A PRO* 3.2 44.9 - - + +
86A VAL* 3.9 17.7 - - + -
245A SER 3.2 22.4 + - - +
246A VAL 3.0 4.8 + - - +
248A VAL* 1.3 77.1 - - - +
250A TYR* 1.3 64.1 + - - +
252A MET* 3.5 6.8 + - - +
253A ASN* 2.9 29.7 + - - -
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Residues in contact with TYR 250 (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 LEU* 3.9 17.9 - - + -
4A ILE* 4.1 10.3 - - + +
29A LEU* 3.6 60.8 + - + -
30A GLY 5.6 0.7 - - - -
31A VAL* 4.7 10.8 - - + -
246A VAL 2.8 11.8 + - - +
247A THR* 3.2 9.4 - - + +
249A LEU* 1.3 74.8 - - - +
251A LEU* 1.3 78.1 - - + +
253A ASN* 2.9 19.0 + - - +
254A LYS* 3.0 52.0 + - + +
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Residues in contact with LEU 251 (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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247A THR* 2.9 37.4 + - + +
248A VAL* 3.9 4.0 - - + +
250A TYR* 1.3 90.1 - - + +
252A MET* 1.3 56.6 + - - +
254A LYS* 4.2 6.3 - - + +
255A ILE* 2.7 56.6 + - + +
260A THR* 3.4 24.0 - - + +
263A MET* 4.0 29.8 - - + -
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Residues in contact with MET 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PRO* 4.3 17.4 - - + +
86A VAL* 4.4 7.9 - - + -
98A TYR* 3.9 22.7 - - + -
99A VAL* 3.6 31.0 - - + -
248A VAL* 3.3 30.1 + - + +
249A LEU* 3.8 8.3 - - - +
250A TYR 3.1 1.0 + - - -
251A LEU* 1.3 77.0 - - - +
253A ASN* 1.3 60.7 + - - +
256A GLY* 3.3 25.1 - - - -
257A VAL* 3.7 28.4 + - + +
260A THR* 3.6 20.4 - - + +
261A LEU* 4.2 9.9 - - + -
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Residues in contact with ASN 253 (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 LEU* 4.0 23.8 - - + +
4A ILE* 5.2 3.2 - - - +
59A ASN* 3.2 47.6 + - - +
60A GLY* 4.5 1.4 - - - +
84A PRO* 4.3 6.6 - - - +
249A LEU 2.9 23.0 + - - -
250A TYR* 2.9 9.4 + - - +
252A MET* 1.3 82.0 - - - +
254A LYS* 1.3 64.4 - - + +
256A GLY* 4.2 2.8 + - - -
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Residues in contact with LYS 254 (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 LEU* 4.3 14.5 - - + +
250A TYR* 3.0 62.2 + - + +
251A LEU* 3.0 7.8 + - + +
253A ASN* 1.3 81.5 - - + +
255A ILE* 1.3 68.1 + - + +
256A GLY 3.5 0.2 - - - -
290B ASP* 4.6 13.3 + - - -
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Residues in contact with ILE 255 (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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251A LEU* 2.7 43.4 + - + +
254A LYS* 1.3 82.6 - - + +
256A GLY* 1.3 54.7 + - - +
259A ASN* 2.9 49.3 + - + +
260A THR* 3.5 22.0 - - - +
263A MET* 5.7 6.1 - - - -
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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