Contacts of the helix formed by residues 244 - 265 (chain A) in PDB entry 2G4C
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 PRO 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU* 4.2 21.1 - - + +
205A PRO* 4.4 8.5 - - + -
243A THR* 1.3 88.1 - - - +
245A PRO* 1.3 63.5 - - + -
246A ARG 2.9 5.8 + - - -
247A THR* 2.9 18.6 + - - +
248A SER* 2.7 29.1 + - - -
251A TRP* 5.3 0.4 - - - +
326A ASP* 3.3 37.9 - - + +
331A VAL* 4.1 13.0 - - + -
333A PRO* 4.4 4.0 - - + -
334A CYS 4.4 1.1 - - - +
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Residues in contact with PRO 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR 3.8 1.0 - - - +
244A PRO* 1.3 83.9 - - + -
246A ARG* 1.3 64.3 + - - +
248A SER* 3.0 22.1 - - - -
249A ASN* 4.1 3.5 + - - +
308A ASP* 6.1 1.3 - - + +
331A VAL* 4.1 13.7 - - + -
332A VAL 3.7 21.1 - - - +
334A CYS* 3.5 24.2 - - - -
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Residues in contact with ARG 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PRO* 2.9 4.9 + - - +
245A PRO* 1.3 79.1 - - - +
247A THR* 1.3 74.2 + - - +
249A ASN* 4.6 4.0 + - - +
250A GLN* 4.6 4.7 + - - +
326A ASP* 3.1 37.7 + - - +
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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
----------------------------------------------------------
243A THR* 3.7 3.6 - - - -
244A PRO* 2.9 17.2 + - - +
246A ARG* 1.3 93.5 + - - +
248A SER* 1.3 52.1 + - - +
250A GLN* 2.6 40.8 + - + +
251A TRP* 2.7 55.3 + - + +
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 3.6 14.2 + - - +
244A PRO 2.7 9.2 + - - -
245A PRO* 3.0 31.9 - - - -
246A ARG 3.2 0.2 - - - -
247A THR* 1.3 79.1 - - - +
249A ASN* 1.3 60.5 + - - +
250A GLN 2.9 2.4 + - - -
251A TRP* 3.1 11.3 + - - +
252A LEU 3.2 8.8 + - - -
305A ASN* 2.5 38.7 + - - -
334A CYS* 3.6 13.6 - - - +
336A LEU* 3.9 2.3 - - - +
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Residues in contact with ASN 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PRO 4.1 4.0 + - - +
246A ARG 4.6 2.8 + - - +
247A THR 3.5 0.2 - - - -
248A SER* 1.3 79.7 + - - +
250A GLN* 1.3 60.1 + - - +
252A LEU* 3.7 12.1 - - - +
253A ASP* 2.8 25.5 - - - +
285A LYS* 3.4 44.3 - - - +
305A ASN* 3.8 9.9 - - - +
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Residues in contact with GLN 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ARG 4.6 3.9 + - - +
247A THR* 2.6 37.6 + - + +
249A ASN* 1.3 74.3 - - - +
251A TRP* 1.3 58.4 + - - +
253A ASP* 2.8 50.3 + - - +
254A PHE* 3.3 3.5 + - - +
257A ARG* 6.0 0.6 - - - +
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Residues in contact with TRP 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 5.7 3.1 - - - -
124A GLN* 5.2 7.0 - - - -
205A PRO* 3.8 23.3 - - + +
241A TRP* 3.2 33.9 - + + -
243A THR* 3.0 28.4 + - + -
244A PRO* 5.3 0.2 - - - +
247A THR* 2.7 45.0 + - + +
248A SER 3.7 2.7 - - - +
250A GLN* 1.3 70.3 - - - +
252A LEU* 1.3 66.5 + - - +
254A PHE* 2.8 56.5 + + + +
255A TRP* 2.9 19.3 + - + -
336A LEU* 3.6 18.8 - - + -
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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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248A SER 3.2 9.2 + - - +
249A ASN* 3.7 15.7 - - - +
251A TRP* 1.3 78.7 - - - +
253A ASP* 1.3 71.5 + - - +
255A TRP* 3.5 0.9 + - - +
256A LEU* 3.1 19.1 + - - +
285A LYS* 5.0 17.7 - - + +
286A GLY* 5.4 2.0 - - - -
287A ASN* 3.2 24.0 - - - +
303A LEU* 4.0 24.2 - - + -
304A TRP* 4.4 10.1 - - - +
305A ASN* 4.6 12.1 - - + +
336A LEU* 3.3 32.2 - - + +
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Residues in contact with ASP 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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249A ASN* 2.8 26.5 - - - +
250A GLN* 2.8 35.6 + - - +
252A LEU* 1.3 82.2 - - - +
254A PHE* 1.3 68.5 + - - +
256A LEU* 3.1 7.4 + - - +
257A ARG* 3.1 43.9 + - - +
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Residues in contact with PHE 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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122A ARG* 3.4 37.9 - - - -
250A GLN 3.3 2.1 + - - +
251A TRP* 2.8 48.4 + + + +
253A ASP* 1.3 81.2 - - - +
255A TRP* 1.3 81.8 + + - +
257A ARG* 3.2 16.0 + - + +
258A HIS* 2.8 36.1 + + + +
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Residues in contact with TRP 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 4.2 16.2 - - + -
122A ARG* 4.3 19.1 - - - -
125A VAL* 5.6 0.7 - - + -
239A LEU* 3.6 32.8 - - + -
241A TRP* 3.7 42.5 - + + -
251A TRP* 2.9 40.4 + + - +
252A LEU 4.0 2.2 - - - +
254A PHE* 1.3 85.2 - + - +
256A LEU* 1.3 60.5 + - - +
257A ARG 3.1 1.6 - - - -
258A HIS* 3.8 37.0 - + + -
259A ARG* 2.7 43.9 + - - +
303A LEU* 3.8 15.3 - - + -
336A LEU* 4.2 17.9 - - + -
338A VAL* 4.2 10.1 - - + -
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Residues in contact with LEU 256 (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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252A LEU* 3.1 8.5 + - + +
253A ASP* 3.1 10.7 + - - +
255A TRP* 1.3 73.6 - - - +
257A ARG* 1.3 60.5 + - - +
259A ARG* 4.6 0.4 - - - -
260A LEU* 2.8 39.1 + - + +
275A SER* 3.9 26.7 - - - +
276A SER 5.0 0.9 - - - +
277A ASP* 5.7 1.6 - - - +
287A ASN* 3.4 47.1 - - + +
289A LEU* 3.6 30.3 - - + -
303A LEU* 3.6 9.3 - - + +
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Residues in contact with ARG 257 (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 GLN* 6.0 0.6 - - - +
253A ASP* 3.1 35.8 + - - +
254A PHE* 3.2 16.7 + - + +
256A LEU* 1.3 81.3 - - - +
258A HIS* 1.3 52.5 + - - +
260A LEU* 3.6 3.9 - - - +
261A GLN* 2.7 68.5 + - + +
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Residues in contact with HIS 258 (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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117A SER* 2.7 51.0 + - - -
118A VAL* 4.3 2.9 - - + -
121A PHE* 5.1 3.2 - + - -
122A ARG* 4.2 14.9 + - - -
254A PHE* 2.8 33.3 + + + +
255A TRP* 3.6 37.2 - + + +
257A ARG* 1.3 71.9 - - - +
259A ARG* 1.3 73.5 + - - +
261A GLN* 3.3 9.3 + - - +
262A TRP* 2.8 27.6 + + + +
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Residues in contact with ARG 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TRP* 3.6 24.2 - - - +
117A SER* 4.8 1.6 + - - -
118A VAL* 5.4 3.0 - - - +
239A LEU* 6.3 0.4 - - - -
255A TRP* 2.7 38.1 + - + +
256A LEU* 3.9 3.1 - - - +
258A HIS* 1.3 86.3 + - - +
260A LEU* 1.3 68.3 + - - +
262A TRP* 2.9 70.9 + - - +
263A TRP* 3.1 26.3 + - - +
289A LEU* 4.8 7.2 - - + -
301A GLU* 2.6 45.4 + - - +
303A LEU* 4.3 4.5 - - + -
338A VAL* 3.8 22.7 - - + -
340A GLY* 5.8 0.4 - - - -
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Residues in contact with LEU 260 (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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256A LEU* 2.8 27.4 + - + +
257A ARG* 3.7 3.6 - - - +
259A ARG* 1.3 74.7 - - - +
261A GLN* 1.3 64.7 + - + +
262A TRP 3.2 0.2 + - - -
263A TRP* 3.3 12.4 + - + +
264A ARG* 3.4 59.2 + - - +
273A PHE* 3.8 13.9 - - + +
274A SER 4.2 3.8 - - - -
275A SER* 3.6 26.0 - - - +
289A LEU* 3.3 27.9 - - + +
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Residues in contact with GLN 261 (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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257A ARG* 2.7 61.3 + - + +
258A HIS* 3.6 6.8 + - - +
260A LEU* 1.3 74.2 - - + +
262A TRP* 1.3 61.1 + - - +
264A ARG* 3.6 9.6 + - - +
265A LYS* 3.2 23.6 + - - +
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Residues in contact with TRP 262 (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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110A LEU* 3.2 36.8 - - + -
113A GLU* 3.9 13.1 + - + +
114A TRP* 3.2 37.9 - + + +
117A SER* 3.2 35.2 - - - +
258A HIS* 2.8 13.5 + - + +
259A ARG* 2.9 47.2 + - - +
261A GLN* 1.3 74.3 - - - +
263A TRP* 1.3 100.5 + + - +
265A LYS* 3.0 47.9 - - - +
266A PHE* 3.5 21.2 - + - -
342A LEU* 5.1 2.9 - - + -
349A TYR* 5.2 1.3 - - - -
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Residues in contact with TRP 263 (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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110A LEU* 5.2 2.0 - - + -
259A ARG* 3.1 41.5 + - - +
260A LEU* 3.3 8.3 + - + +
262A TRP* 1.3 93.3 - + - +
264A ARG* 1.3 63.1 + - - +
265A LYS 3.5 0.2 + - - -
266A PHE 3.7 1.2 + - - -
267A ALA* 3.8 5.9 + - - +
273A PHE* 3.6 35.5 - + + -
289A LEU* 4.6 7.2 - - + -
300A ILE* 3.6 33.1 - - + +
301A GLU* 2.7 35.6 + - + +
340A GLY* 5.0 4.3 - - - -
341A ASP 4.0 9.9 - - - -
342A LEU* 5.2 7.4 - - + -
345A GLY* 3.4 34.1 - - - -
349A TYR* 2.3 50.6 + + - -
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Residues in contact with ARG 264 (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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260A LEU* 3.4 46.5 + - - +
261A GLN* 3.9 10.8 - - - +
262A TRP 3.3 0.6 - - - -
263A TRP* 1.3 72.2 - - - +
265A LYS* 1.3 57.2 + - - +
266A PHE 2.9 3.3 + - - -
267A ALA* 2.8 36.5 + - - +
270A PRO* 3.4 34.3 + - + +
271A SER 5.7 0.4 + - - -
273A PHE* 2.8 37.0 + - + -
274A SER* 4.0 6.5 - - - +
275A SER 4.7 0.6 - - - +
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Residues in contact with LYS 265 (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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113A GLU* 5.6 1.0 - - - +
117A SER* 4.1 7.3 + - - -
121A PHE* 5.8 6.3 - - - -
261A GLN 3.2 11.5 + - - +
262A TRP* 3.0 49.3 + - - +
264A ARG* 1.3 74.7 - - - +
266A PHE* 1.3 79.2 + - + +
267A ALA 3.6 1.0 - - - +
375A HIS* 3.4 15.2 + - - +
482A ALA 5.2 0.2 - - - +
483A LYS* 4.9 16.8 - - + +
485A VAL* 5.2 8.6 - - - +
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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
------------------------------------------------------------
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