Contacts of the helix formed by residues 240 - 255 (chain A) in PDB entry 1C3Q
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 GLY 240 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 4.8 5.8 - - - -
236A THR* 3.3 10.4 + - - +
237A ALA 4.6 3.8 + - - -
238A ASP 3.6 1.6 - - - -
239A LYS* 1.3 80.2 - - - +
241A PRO* 1.3 73.2 - - - +
243A SER 3.3 0.7 + - - -
244A PHE* 3.1 18.7 + - - +
250B ASN* 3.1 16.4 - - - +
253B SER* 5.0 0.7 - - - -
254B THR* 4.9 5.2 - - - -
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Residues in contact with PRO 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 4.4 10.5 - - + -
192A LYS* 3.8 36.6 - - + +
193A VAL* 4.2 5.2 - - + +
240A GLY* 1.3 82.0 - - - +
242A GLY* 1.3 62.3 + - - +
244A PHE* 3.7 9.2 - - + +
245A GLN* 3.1 25.0 + - - +
38B ALA* 3.6 32.8 - - + -
249B LEU* 3.8 5.2 - - + +
250B ASN* 4.2 1.3 - - - +
253B SER* 3.4 25.4 - - - +
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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
----------------------------------------------------------
241A PRO* 1.3 79.6 - - - +
243A SER* 1.3 65.9 + - - +
245A GLN* 3.4 5.1 + - - +
246A ILE* 3.4 25.3 + - - +
246B ILE* 3.7 13.7 - - - +
249B LEU* 3.9 30.5 - - - +
250B ASN* 2.9 10.6 + - - -
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Residues in contact with SER 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR* 3.4 18.2 - - - -
239A LYS* 3.6 28.4 - - - +
240A GLY 3.3 1.1 + - - -
242A GLY* 1.3 75.2 - - - +
244A PHE* 1.3 58.4 + - - +
246A ILE* 3.3 7.0 + - - +
247A GLU* 2.9 30.1 + - - +
246B ILE* 4.1 9.2 - - - +
247B GLU* 4.7 1.4 + - - -
250B ASN* 2.7 29.7 + - - +
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Residues in contact with PHE 244 (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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187A HIS* 4.8 2.7 - - + -
189A LEU* 3.6 45.5 - - + -
190A LEU* 3.6 35.7 - - + -
193A VAL* 3.7 19.7 - - + -
229A ALA* 3.5 31.0 - - + -
232A ALA* 3.8 9.2 - - + -
233A ALA* 3.5 22.7 - - + -
236A THR* 2.8 23.9 - - + +
240A GLY 3.1 8.4 + - - +
241A PRO* 3.7 6.3 - - + +
242A GLY 3.2 0.2 - - - -
243A SER* 1.3 75.3 - - - +
245A GLN* 1.3 57.3 + - - +
247A GLU* 3.1 2.4 + - - +
248A LEU* 2.8 35.0 + - + +
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Residues in contact with GLN 245 (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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31A PHE* 3.5 32.2 - - + -
193A VAL* 3.8 20.3 - - + +
241A PRO 3.1 18.6 + - - +
242A GLY 3.6 4.5 + - - +
243A SER 3.3 0.2 - - - -
244A PHE* 1.3 74.3 - - - +
246A ILE* 1.3 76.2 + - + +
248A LEU* 3.2 17.5 + - - +
249A LEU* 3.3 18.4 + - + +
30B ASN* 4.7 4.6 - - - +
34B ASN* 3.5 32.8 + - - +
246B ILE* 5.6 2.8 - - - +
249B LEU* 4.3 15.2 - - - +
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Residues in contact with ILE 246 (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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242A GLY 3.5 13.0 - - - +
243A SER* 3.3 8.5 + - - +
244A PHE 3.2 0.6 - - - -
245A GLN* 1.3 88.1 - - - +
247A GLU* 1.3 64.0 + - - +
249A LEU* 3.2 18.5 + - + +
250A ASN* 3.1 20.1 + - - +
246B ILE* 3.8 22.7 - - + -
242C GLY* 3.5 26.8 - - - +
243C SER* 3.6 14.4 - - - +
245C GLN* 5.1 4.0 - - - +
246C ILE* 3.6 31.2 - - + -
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Residues in contact with GLU 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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232A ALA* 3.7 26.9 - - + +
235A GLN* 4.6 14.2 - - + +
236A THR* 3.5 20.2 + - - +
243A SER 2.9 10.4 + - - +
244A PHE 3.1 3.8 + - - +
246A ILE* 1.3 75.7 - - - +
248A LEU* 1.3 60.8 + - - +
250A ASN* 3.3 22.4 + - - +
251A LYS* 2.5 63.0 + - - +
239C LYS* 5.0 1.2 - - - +
243C SER* 4.8 0.9 + - - -
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.1 19.3 - - + -
190A LEU* 3.7 27.4 - - + -
193A VAL* 5.8 2.5 - - + -
196A ALA* 5.8 0.4 - - + -
225A TYR* 3.9 20.9 - - + +
228A ALA* 4.3 4.0 - - + -
229A ALA* 4.1 30.3 - - + +
232A ALA* 3.7 8.5 - - + +
244A PHE* 2.8 19.5 + - + +
245A GLN* 3.2 11.9 + - - +
247A GLU* 1.3 76.6 - - - +
249A LEU* 1.3 58.1 + - + +
251A LYS* 3.3 1.1 + - - +
252A LEU* 2.9 48.5 + - + +
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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
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31A PHE* 3.8 28.9 - - + -
34A ASN* 4.0 13.7 - - + +
35A GLY* 3.6 34.8 - - - +
38A ALA* 3.2 26.9 - - + +
245A GLN* 3.6 16.2 - - - +
246A ILE* 3.2 16.1 + - + +
248A LEU* 1.3 78.6 - - - +
250A ASN* 1.3 63.1 + - - +
252A LEU* 3.5 10.0 + - + -
253A SER* 3.5 1.9 + - - -
241C PRO* 3.9 1.4 - - - +
242C GLY* 3.9 17.5 - - - +
245C GLN* 4.1 22.2 - - - +
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Residues in contact with ASN 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ILE* 3.1 16.2 + - - +
247A GLU* 3.5 36.5 + - - +
248A LEU 3.2 0.2 - - - -
249A LEU* 1.3 77.2 - - - +
251A LYS* 1.3 59.5 + - - +
253A SER* 3.1 8.0 + - - -
254A THR* 2.9 30.2 + - - +
239C LYS* 3.4 22.8 + - - +
240C GLY* 3.1 11.1 - - - -
241C PRO* 4.4 0.9 - - - -
242C GLY 2.8 24.6 + - - -
243C SER* 2.8 31.3 + - - +
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Residues in contact with LYS 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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228A ALA* 3.5 23.8 - - + +
231A LEU* 4.0 31.9 - - + -
232A ALA* 3.8 17.7 - - + +
235A GLN* 5.4 5.5 - - - +
247A GLU* 2.5 52.8 + - - +
248A LEU 3.9 2.9 - - - +
250A ASN* 1.3 77.3 - - - +
252A LEU* 1.3 55.6 + - - +
253A SER 2.9 5.4 - - - -
254A THR* 3.5 14.9 + - - +
255A VAL* 2.7 36.4 + - + +
239C LYS 5.1 3.0 + - - -
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Residues in contact with LEU 252 (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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14A ARG* 3.0 19.0 + - - -
35A GLY* 4.0 19.1 - - - +
38A ALA* 3.8 8.5 - - + -
39A LEU* 3.4 35.7 - - + +
199A LEU* 4.1 25.4 - - + -
203A VAL* 5.4 3.8 - - + -
224A SER 5.2 1.1 - - - +
225A TYR* 3.8 28.0 - - + +
228A ALA* 3.9 16.2 - - + -
248A LEU* 2.9 35.7 + - + +
249A LEU* 3.8 8.3 - - + +
250A ASN 3.3 0.2 - - - -
251A LYS* 1.3 75.8 - - - +
253A SER* 1.3 56.0 + - - +
255A VAL* 3.9 3.9 - - + +
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Residues in contact with SER 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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14A ARG* 3.5 12.9 + - - +
38A ALA 3.2 17.8 + - - -
249A LEU 3.5 1.9 + - - -
250A ASN 3.1 10.1 + - - -
251A LYS 2.9 0.6 - - - -
252A LEU* 1.3 82.0 - - - +
254A THR* 1.3 64.2 + - - +
255A VAL 3.6 0.2 - - - -
240C GLY* 5.1 0.2 - - - -
241C PRO* 3.6 32.6 - - - +
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Residues in contact with THR 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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250A ASN 2.9 18.2 + - - +
251A LYS* 3.5 22.9 + - - +
253A SER* 1.3 81.9 - - - +
255A VAL* 1.3 68.3 + - - +
256A THR* 3.2 16.5 + - - +
259A ASP* 4.2 1.8 - - - +
238C ASP 4.7 8.3 - - - +
239C LYS 4.0 17.3 - - - +
240C GLY* 5.0 2.0 - - - -
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Residues in contact with VAL 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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10A LEU* 4.2 11.7 - - + -
14A ARG* 2.7 52.2 + - - +
39A LEU* 5.8 1.1 - - + -
224A SER* 4.9 5.8 - - - +
227A VAL* 4.0 19.1 - - + -
228A ALA* 4.5 12.3 - - + +
231A LEU* 4.3 9.2 - - + -
251A LYS* 2.7 27.1 + - - +
252A LEU* 3.9 7.6 - - + +
254A THR* 1.3 72.1 + - - +
256A THR* 1.3 61.5 + - - +
259A ASP* 3.6 25.8 - - + +
260A VAL* 4.3 7.0 - - + -
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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