Contacts of the helix formed by residues 265 - 283 (chain A) in PDB entry 1GM5
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 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 3.7 10.3 - - - -
264A ILE* 1.3 78.7 - - - +
266A GLN* 1.3 55.0 + - - +
267A LYS* 2.7 16.5 + - - +
268A GLN* 2.8 21.4 + - - +
269A MET* 2.5 36.0 + - - +
10Y G 3.1 21.9 + - - -
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Residues in contact with GLN 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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148A ARG* 5.2 3.0 + - - +
256A PRO 3.3 9.5 + - - -
257A ILE* 3.4 15.8 - - + +
258A TYR* 2.6 46.6 + - - +
260A LEU* 3.5 18.6 - - + +
265A SER* 1.3 73.5 + - - +
267A LYS* 1.3 66.6 + - - +
269A MET* 4.4 1.6 - - - +
270A ARG* 2.6 70.2 + - - +
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Residues in contact with LYS 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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242A GLU* 2.8 46.8 + - + +
244A THR* 5.3 8.7 - - - +
265A SER* 2.7 9.6 + - - +
266A GLN* 1.3 78.2 - - - +
268A GLN* 1.3 64.1 + - - +
270A ARG* 3.8 10.2 - - - +
271A LYS* 3.3 20.1 + - - +
9Y C 3.4 46.3 + - - +
10Y G 3.5 21.3 - - - +
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Residues in contact with GLN 268 (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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127A ARG* 3.0 33.2 + - - +
263A GLY 3.3 4.7 + - - +
264A ILE* 3.0 28.8 - - + +
265A SER* 2.8 23.5 + - - +
266A GLN 2.9 0.2 - - - -
267A LYS* 1.3 72.6 - - - +
269A MET* 1.3 71.9 + - - +
270A ARG 2.6 2.9 + - - -
271A LYS* 3.0 13.4 + - - +
272A ILE* 2.8 14.1 + - - +
9Y C 3.9 21.3 + - - +
10Y G 3.8 18.9 - - - +
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Residues in contact with MET 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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131A LEU* 4.1 26.0 - - + -
134A LEU* 5.3 5.4 - - + -
136A ILE* 5.3 2.5 - - + -
145A PHE* 4.6 6.1 - - + -
258A TYR* 3.8 21.3 - - + -
259A ARG 4.2 6.7 - - - +
260A LEU* 3.6 26.5 - - + -
264A ILE* 3.4 18.2 - - + +
265A SER 2.5 14.7 + - - +
266A GLN* 4.1 2.9 - - - +
268A GLN* 1.3 75.0 - - - +
270A ARG* 1.3 56.6 + - - +
272A ILE* 2.0 35.8 - - - +
273A PHE* 2.6 60.7 - - + -
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Residues in contact with ARG 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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151A GLU* 4.0 16.0 + - - -
153A ARG* 4.3 11.3 - - - +
242A GLU* 5.2 6.7 + - - -
255A LEU* 2.6 37.7 + - + +
256A PRO* 2.6 44.3 + - + +
257A ILE* 4.0 8.9 - - - +
258A TYR* 4.4 7.9 - - + -
266A GLN* 2.6 49.3 + - - +
267A LYS* 3.8 9.2 - - - +
268A GLN 2.6 2.2 + - - -
269A MET* 1.3 66.8 - - - +
271A LYS* 1.3 50.9 + - - +
272A ILE 2.8 4.0 - - - -
273A PHE* 2.6 7.6 + - - +
274A GLU* 2.6 52.5 + - + +
310A PHE* 4.6 0.6 - - + -
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Residues in contact with LYS 271 (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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121A LYS* 5.4 0.4 - - - +
122A GLY* 4.1 17.0 - - - -
267A LYS 3.3 13.7 + - - +
268A GLN* 3.0 4.7 + - - +
270A ARG* 1.3 77.4 - - - +
272A ILE* 1.3 65.3 + - + +
274A GLU* 3.5 17.8 + - + +
275A GLU* 3.0 56.0 + - + +
8Y T 4.6 22.9 - - - +
9Y C 4.0 21.8 - - - +
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Residues in contact with ILE 272 (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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121A LYS 4.5 9.6 - - - +
122A GLY* 5.4 2.9 - - - -
123A VAL* 3.8 30.7 - - + +
127A ARG* 5.5 8.5 - - - -
131A LEU* 4.0 18.8 - - + -
142A LEU* 5.2 8.5 - - + +
264A ILE* 5.6 2.5 - - + -
268A GLN 2.8 6.7 + - - +
269A MET* 2.0 65.3 - - + +
271A LYS* 1.3 84.1 - - + +
273A PHE* 1.3 64.6 + - + -
275A GLU* 4.4 4.3 - - - -
276A ASN* 2.8 30.7 + - - +
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Residues in contact with PHE 273 (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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131A LEU* 6.1 0.2 - - + -
136A ILE* 4.9 3.1 - - + -
142A LEU* 3.9 33.4 - - + -
145A PHE* 4.1 20.2 - + - -
258A TYR* 3.4 51.8 - + + +
269A MET* 2.6 66.3 + - + -
270A ARG 2.6 11.3 + - - +
272A ILE* 1.3 75.9 - - + +
274A GLU* 1.3 63.8 + - - +
275A GLU 3.0 2.5 - - - -
277A ILE* 3.0 53.5 + - + +
278A PRO* 3.8 0.7 - - - +
309A HIS* 3.8 1.6 - + - -
310A PHE* 4.0 7.0 - - + -
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Residues in contact with GLU 274 (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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253A ARG* 5.8 2.8 + - - -
255A LEU* 6.1 1.7 - - - +
270A ARG* 2.6 40.4 + - + +
271A LYS* 3.5 17.6 + - + +
273A PHE* 1.3 74.4 - - - +
275A GLU* 1.3 61.2 + - + +
278A PRO* 3.7 15.8 - - - +
310A PHE* 3.5 30.2 - - + -
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Residues in contact with GLU 275 (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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121A LYS* 3.6 38.1 + - + +
122A GLY* 4.4 3.1 - - - -
271A LYS* 3.0 60.0 + - + +
272A ILE* 4.4 2.8 - - - -
273A PHE 3.0 0.8 - - - -
274A GLU* 1.3 82.1 - - + +
276A ASN* 1.3 71.3 + - - +
278A PRO* 4.5 2.0 - - - -
279A SER* 4.6 7.1 - - - -
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Residues in contact with ASN 276 (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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119A TYR 4.8 0.2 - - - +
120A ALA* 3.6 10.1 - - - -
121A LYS* 2.7 44.8 + - - +
142A LEU* 4.5 10.1 - - + -
272A ILE* 2.8 22.1 + - - +
273A PHE 3.2 1.6 + - - -
275A GLU* 1.3 93.5 - - - +
277A ILE* 1.3 71.6 + - - +
278A PRO* 3.2 3.4 - - - -
279A SER* 2.9 17.4 + - - +
280A LEU* 2.9 29.9 + - + +
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Residues in contact with ILE 277 (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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142A LEU* 3.8 18.4 - - + +
143A LEU* 3.6 20.0 - - + -
273A PHE* 3.0 54.0 + - + +
276A ASN* 1.3 77.5 - - - +
278A PRO* 1.3 75.7 - - + +
280A LEU* 4.4 2.7 - - - +
281A CYS* 2.8 32.6 + - - +
306A TYR* 3.9 26.2 - - + -
309A HIS* 4.0 26.7 - - + +
310A PHE* 5.1 2.7 - - + -
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Residues in contact with PRO 278 (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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104A LEU* 4.3 21.2 - - + +
273A PHE 3.8 1.8 - - - +
274A GLU* 3.7 21.3 - - - +
275A GLU 4.5 0.9 - - - -
276A ASN* 3.3 4.9 - - - +
277A ILE* 1.3 100.0 - - + +
279A SER* 1.3 67.2 + - - +
281A CYS* 3.6 2.8 - - + +
282A CYS* 3.4 21.6 + - - +
306A TYR* 4.4 16.8 - - + +
310A PHE* 6.1 3.1 - - + -
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Residues in contact with SER 279 (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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275A GLU 4.6 4.7 - - - -
276A ASN* 2.9 17.7 + - - +
278A PRO* 1.3 80.8 - - - +
280A LEU* 1.3 80.4 + - - +
282A CYS* 3.2 13.1 - - - +
283A SER* 3.9 4.0 + - - -
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Residues in contact with LEU 280 (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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111A VAL* 5.0 13.2 - - + +
112A ASP* 5.9 1.1 - - - +
120A ALA* 6.4 0.4 - - - -
139A LEU* 3.4 44.6 - - + -
142A LEU* 4.4 14.6 - - + -
143A LEU* 4.4 20.9 - - + -
276A ASN* 2.9 33.6 + - + +
277A ILE 3.0 3.2 + - - +
279A SER* 1.3 77.7 - - - +
281A CYS* 1.3 72.9 - - - +
282A CYS 2.3 3.6 + - - -
283A SER* 2.5 24.6 + - - +
284A LEU* 5.2 0.9 - - + -
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Residues in contact with CYS 281 (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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104A LEU* 3.5 17.7 - - + -
143A LEU* 4.4 15.0 - - - +
277A ILE* 2.8 29.9 + - - +
278A PRO 3.6 0.4 - - - +
280A LEU* 1.3 77.6 - - - +
282A CYS* 1.3 54.5 + - - +
283A SER 2.7 11.3 + - - -
284A LEU* 3.1 23.3 - - - +
302A LYS* 3.5 15.2 - - - +
305A TYR* 3.6 12.1 - - - -
306A TYR* 2.9 42.6 - - - -
309A HIS* 5.9 0.2 - - - -
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Residues in contact with CYS 282 (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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104A LEU* 4.4 13.2 - - - -
106A CYS* 2.0 56.4 - - - -
107A SER 4.3 4.5 - - - +
110A GLU* 5.6 3.6 - - - +
278A PRO 3.4 9.6 + - - -
279A SER* 3.2 15.0 + - - +
280A LEU 2.3 7.5 + - - -
281A CYS* 1.3 75.5 - - - +
283A SER* 1.3 58.0 + - - +
284A LEU 3.4 6.1 + - - +
302A LYS* 4.5 17.1 - - - +
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Residues in contact with SER 283 (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 GLU* 3.7 29.9 - - - -
111A VAL 3.7 10.1 + - - -
112A ASP* 3.2 32.8 - - - +
279A SER 3.9 5.9 + - - -
280A LEU* 2.5 18.6 + - - +
281A CYS 3.4 0.2 - - - +
282A CYS* 1.3 68.4 - - - +
284A LEU* 1.3 87.4 - - - +
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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