Contacts of the helix formed by residues 251 - 270 (chain A) in PDB entry 2GER
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 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A GLY* 6.2 1.6 - - - -
228A LYS* 5.8 10.1 - - - +
246A GLU* 2.8 50.3 + - - +
249A GLY* 4.7 2.2 - - - -
250A PHE* 1.3 83.0 - - + +
252A SER* 1.3 71.7 + - - +
254A LEU* 2.8 23.3 + - - +
255A ILE* 3.3 15.8 + - + +
186C ASP* 4.8 11.5 + - - -
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Residues in contact with SER 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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249A GLY* 2.8 19.4 + - - -
251A ARG* 1.3 79.9 - - - +
253A LEU* 1.3 59.5 + - - +
254A LEU 2.3 17.3 + - - -
255A ILE* 2.7 23.8 + - - +
256A ASN* 3.3 24.0 + - - +
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Residues in contact with LEU 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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248A GLY 4.1 12.6 - - - +
249A GLY* 2.9 20.0 + - - +
250A PHE* 4.1 7.9 - - + +
251A ARG 3.3 0.4 + - - -
252A SER* 1.3 74.6 - - - +
254A LEU* 1.3 62.9 + - - +
256A ASN* 4.2 20.4 - - - +
257A ALA* 3.8 14.1 + - - +
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Residues in contact with LEU 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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180A TYR* 4.7 27.8 - - + +
250A PHE* 3.5 47.8 - - + +
251A ARG* 2.8 13.5 + - - +
252A SER 2.3 16.0 + - - -
253A LEU* 1.3 74.4 - - + +
255A ILE* 1.3 64.2 + - + +
257A ALA* 3.2 8.2 + - + +
258A VAL* 3.0 23.9 + - - +
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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 ARG* 3.6 23.3 - - + +
252A SER* 2.7 14.5 + - - +
254A LEU* 1.3 73.8 - - + +
256A ASN* 1.3 57.7 + - - +
257A ALA 2.6 5.0 + - - -
258A VAL* 2.6 35.0 + - + +
259A GLU* 2.8 19.9 + - + +
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Residues in contact with ASN 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 SER* 3.3 29.6 + - - +
253A LEU* 4.2 20.0 - - - +
255A ILE* 1.3 78.2 - - - +
257A ALA* 1.3 56.8 + - - +
259A GLU* 4.0 15.2 - - - +
260A ALA* 2.9 30.7 + - - +
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Residues in contact with ALA 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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180A TYR* 2.8 39.6 + - + -
253A LEU 3.8 13.4 + - - +
254A LEU* 3.2 13.1 + - + +
255A ILE 2.6 5.7 + - - -
256A ASN* 1.3 75.8 - - - +
258A VAL* 1.3 58.5 + - - +
260A ALA* 3.9 3.7 - - - +
261A SER* 3.0 19.8 + - - -
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Residues in contact with VAL 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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169A ALA* 5.5 3.1 - - - +
172A GLY* 4.0 4.5 - - - +
173A LEU* 3.2 49.6 - - + +
180A TYR* 4.1 11.2 - - + -
254A LEU 3.0 12.9 + - - +
255A ILE* 2.6 20.2 + - + +
257A ALA* 1.3 71.2 - - - +
259A GLU* 1.3 56.5 + - + +
261A SER* 3.0 5.4 + - - -
262A CYS* 2.7 38.2 + - + +
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Residues in contact with GLU 259 (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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255A ILE* 2.8 21.3 + - + +
256A ASN* 4.0 13.9 - - - +
258A VAL* 1.3 82.6 - - + +
260A ALA* 1.3 53.8 + - - +
262A CYS* 3.4 5.0 - - - +
263A ILE* 2.7 62.5 + - + +
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Residues in contact with ALA 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 ASN 2.9 19.3 + - - +
257A ALA* 3.9 5.4 - - - +
259A GLU* 1.3 77.4 - - - +
261A SER* 1.3 68.4 + - - +
263A ILE* 3.6 7.3 - - - +
264A ARG* 2.8 26.2 + - - +
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Residues in contact with SER 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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171A THR* 3.8 2.8 + - - -
172A GLY* 3.2 16.0 - - - -
176A SER* 2.9 22.7 + - - -
180A TYR* 3.2 12.3 - - - -
257A ALA 3.0 17.0 + - - -
258A VAL 3.0 4.8 + - - -
260A ALA* 1.3 80.3 - - - +
262A CYS* 1.3 66.0 - - - +
264A ARG* 3.3 6.9 + - - +
265A THR* 3.2 19.3 + - - -
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Residues in contact with CYS 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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168A ASP 3.5 26.2 - - - +
169A ALA* 3.6 16.2 - - - +
172A GLY* 4.0 1.5 - - - -
258A VAL* 2.7 21.9 + - + +
259A GLU* 3.4 8.7 - - - +
261A SER* 1.3 71.5 - - - +
263A ILE* 1.3 57.8 + - - +
265A THR* 2.7 28.5 + - - -
266A ARG* 2.9 48.6 + - - +
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Residues in contact with ILE 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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259A GLU* 2.7 53.6 + - + +
260A ALA* 3.6 6.5 - - - +
262A CYS* 1.3 75.7 - - + +
264A ARG* 1.3 62.3 + - - +
266A ARG* 3.4 22.6 + - + +
267A GLU* 3.1 35.8 + - + +
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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 ALA 2.8 20.6 + - - +
261A SER* 3.6 6.5 - - - +
262A CYS 3.0 0.2 + - - -
263A ILE* 1.3 73.4 - - - +
265A THR* 1.3 64.3 + - - +
267A GLU* 2.8 35.9 + - - +
268A LEU* 2.9 56.8 + - + +
271A MET* 5.7 3.5 - - - -
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Residues in contact with THR 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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97A ALA* 4.2 14.8 - - - +
98A GLY* 3.5 20.9 - - - +
119A ARG* 4.7 0.2 - - - +
168A ASP* 3.0 33.2 - - + +
171A THR* 4.0 20.7 + - - +
261A SER* 3.2 9.1 + - - -
262A CYS 2.7 16.8 + - - -
264A ARG* 1.3 71.8 - - - +
266A ARG* 1.3 67.6 + - - +
267A GLU 3.3 0.2 + - - -
268A LEU* 3.8 10.4 - - - +
269A GLN* 3.3 18.9 + - - +
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Residues in contact with ARG 266 (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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165A ASP 4.7 5.7 + - - -
168A ASP* 3.2 30.9 + - + +
169A ALA* 4.9 7.1 - - - +
262A CYS* 2.9 40.4 + - - +
263A ILE* 3.5 21.3 - - + +
264A ARG 3.2 0.2 - - - -
265A THR* 1.3 79.6 - - - +
267A GLU* 1.3 64.0 - - + +
269A GLN* 3.2 13.6 + - - +
270A SER* 2.9 29.7 + - - +
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Residues in contact with GLU 267 (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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263A ILE* 3.1 23.7 + - + +
264A ARG* 2.8 39.4 + - - +
266A ARG* 1.3 77.9 - - + +
268A LEU* 1.3 67.8 + - - +
269A GLN 2.7 2.4 + - - -
270A SER* 2.9 16.4 + - - -
271A MET* 3.0 19.7 + - + +
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A PRO* 4.7 29.6 - - + +
97A ALA* 5.3 9.9 - - + +
98A GLY* 6.2 0.2 - - - -
264A ARG* 2.9 62.9 + - + +
265A THR* 3.8 10.5 - - - +
267A GLU* 1.3 76.4 - - - +
269A GLN* 1.3 58.1 + - - +
271A MET* 3.2 39.8 - - + +
272A ALA* 3.4 9.4 + - - +
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Residues in contact with GLN 269 (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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72A PRO* 6.5 0.7 - - - -
97A ALA 5.2 0.4 - - - +
98A GLY* 2.3 53.8 - - - +
99A VAL* 4.3 6.7 - - + +
100A THR* 4.5 10.8 - - - +
119A ARG* 4.0 2.6 + - - -
168A ASP* 3.1 29.4 + - - +
265A THR 3.3 4.1 + - - +
266A ARG* 3.2 13.5 + - - +
267A GLU 2.7 4.0 + - - -
268A LEU* 1.3 72.9 - - - +
270A SER* 1.3 68.9 + - - +
271A MET 2.6 15.9 + - - -
272A ALA* 2.7 17.3 + - - +
273A ASP* 3.1 20.6 + - - +
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Residues in contact with SER 270 (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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266A ARG* 2.9 25.3 + - - +
267A GLU* 3.2 7.4 - - - -
269A GLN* 1.3 81.2 + - - +
271A MET* 1.3 55.9 + - - +
273A ASP* 2.9 23.2 + - - -
274A GLN* 5.6 3.9 - - - +
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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