Contacts of the helix formed by residues 260 - 278 (chain B) in PDB entry 1GG3
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 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.9 21.6 + - - -
236B SER* 3.8 11.9 - - - -
258B LEU* 3.2 1.9 - - - +
259B PRO* 1.3 83.0 - - - +
261B TYR* 1.3 65.7 + - - +
262B ARG* 2.9 15.4 + - - +
263B ALA* 2.9 30.5 + - - +
264B ALA* 2.9 14.0 + - - +
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Residues in contact with TYR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 4.2 16.1 - - - +
32A GLU* 5.5 0.9 - - + -
33A HIS* 3.1 62.8 - + + +
36A LEU* 3.1 32.3 - - + -
37A LEU 2.8 24.4 + - - -
38A GLU* 3.2 23.6 - - - -
40A ASP* 5.4 2.2 - - - -
233B TYR* 3.9 5.7 - + + -
235B ARG* 3.4 33.0 - - - +
236B SER* 4.1 2.8 - - - +
260B SER* 1.3 74.7 - - - +
262B ARG* 1.3 65.3 + - + +
264B ALA* 3.7 1.0 - - - +
265B LYS* 2.9 40.7 + - + +
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Residues in contact with ARG 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 2.9 63.0 + - + +
38A GLU* 2.9 29.4 + - - +
89A GLU* 2.9 28.5 + - - -
91A ILE* 3.3 7.7 - - - +
260B SER* 3.1 11.8 + - - +
261B TYR* 1.3 88.6 - - + +
263B ALA* 1.3 59.4 + - - +
265B LYS* 3.3 5.1 + - - +
266B LYS* 2.9 34.2 + - + +
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B HIS* 5.3 0.9 + - - -
258B LEU* 3.8 17.1 - - + +
259B PRO* 3.9 12.3 - - + -
260B SER* 2.9 28.4 + - - +
262B ARG* 1.3 77.1 - - - +
264B ALA* 1.3 52.9 + - - +
266B LYS* 3.1 13.4 - - + +
267B LEU* 2.8 35.0 + - - +
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B TYR* 4.0 14.4 - - + -
235B ARG 3.4 25.8 - - - +
236B SER* 4.1 7.6 - - - -
237B SER 4.1 2.2 - - - +
238B PHE* 4.1 2.9 - - + +
258B LEU* 3.0 22.6 - - + +
260B SER 2.9 11.1 + - - +
261B TYR 3.7 1.1 - - - +
263B ALA* 1.3 75.0 - - - +
265B LYS* 1.3 55.3 + - - +
267B LEU* 3.2 1.2 + - - +
268B TRP* 2.7 37.6 + - - +
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Residues in contact with LYS 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A HIS* 4.0 27.3 + - + +
34A LEU* 4.7 10.5 + - - +
36A LEU* 5.4 8.3 - - + +
60B LYS* 5.6 9.1 - - - +
233B TYR* 3.3 41.7 + - + +
261B TYR* 2.9 29.9 + - + +
262B ARG* 3.6 5.2 - - - +
264B ALA* 1.3 76.8 - - - +
266B LYS* 1.3 56.5 + - - +
268B TRP* 3.7 13.5 - - + -
269B LYS* 3.0 32.4 + - + +
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B SER* 3.7 25.0 + - - -
53B LYS 2.8 31.2 + - - -
54B THR* 3.9 18.3 + - + +
192B HIS* 4.2 25.3 + - + +
262B ARG* 2.9 18.5 + - + +
263B ALA* 3.1 15.3 - - - +
265B LYS* 1.3 74.5 - - - +
267B LEU* 1.3 65.4 + - - +
269B LYS* 3.1 6.6 + - - +
270B VAL* 3.1 28.4 + - + +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B HIS* 4.1 30.7 - - + +
204B LEU* 3.4 37.5 - - + -
206B VAL* 4.0 14.1 - - + -
211B LEU* 5.3 0.4 - - + -
238B PHE* 3.8 16.6 - - + -
258B LEU* 3.6 28.3 - - + -
263B ALA 2.8 19.2 + - - +
264B ALA 3.7 3.6 - - - +
266B LYS* 1.3 73.9 - - - +
268B TRP* 1.3 60.3 + - - +
270B VAL* 4.7 1.6 - - + -
271B CYS* 3.2 36.1 + - - -
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Residues in contact with TRP 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 3.1 39.5 + - + -
232B SER* 3.5 15.5 - - - +
233B TYR* 3.8 34.5 - + + -
238B PHE* 3.5 14.3 - - + -
264B ALA 2.7 18.0 + - - +
265B LYS* 3.7 17.5 - - + +
267B LEU* 1.3 76.9 - - - +
269B LYS* 1.3 95.6 + - + +
271B CYS* 3.5 1.2 + - - +
272B VAL* 3.0 52.8 + - + +
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Residues in contact with LYS 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP* 3.2 31.2 + - - -
60B LYS* 4.8 11.7 - - - +
265B LYS* 3.0 22.1 + - + +
266B LYS* 3.1 6.0 + - - +
268B TRP* 1.3 95.5 - - + +
270B VAL* 1.3 67.1 + - + +
272B VAL* 3.3 4.9 + - + +
273B GLU* 3.0 49.3 + - + +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TRP* 4.2 25.8 - - + +
190B ASP* 4.0 20.2 - - - +
192B HIS* 4.3 11.4 - - + +
206B VAL* 3.6 33.9 - - + -
266B LYS* 3.1 21.0 + - + +
267B LEU 4.1 3.1 - - - +
269B LYS* 1.3 77.3 - - + +
271B CYS* 1.3 58.8 + - - +
273B GLU* 3.0 11.9 + - - +
274B HIS* 2.9 37.4 + - + +
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Residues in contact with CYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 3.5 26.7 - - - -
211B LEU* 4.1 9.0 - - - -
225B TRP* 3.5 24.6 - - + -
231B ILE* 3.7 18.1 - - + +
238B PHE* 3.9 11.7 - - + -
240B ILE* 5.8 0.7 - - + -
267B LEU* 3.2 32.6 + - - +
268B TRP 3.8 3.4 - - - +
270B VAL* 1.3 80.6 - - - +
272B VAL* 1.3 57.0 + - - +
275B HIS* 3.0 31.0 + - - +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 4.0 19.3 - - + +
268B TRP* 3.0 57.1 + - + +
269B LYS* 3.8 5.4 - - - +
271B CYS* 1.3 76.6 - - - +
273B GLU* 1.3 61.8 + - + +
275B HIS* 3.9 2.0 - - - +
276B THR* 2.8 41.0 + - - +
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TRP* 5.5 6.5 - - - +
78B LYS* 2.9 39.8 + - - -
79B PHE* 3.5 16.7 - - + -
269B LYS* 3.0 50.0 + - + +
270B VAL* 3.0 7.8 + - - +
272B VAL* 1.3 78.8 - - + +
274B HIS* 1.3 59.0 + - + +
276B THR* 3.8 4.3 - - - -
277B PHE* 2.9 29.8 + - - +
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Residues in contact with HIS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LYS* 3.5 24.3 + - + +
79B PHE* 3.4 25.6 - + - -
80B TYR 5.6 1.8 - - - -
188B GLY 4.9 4.5 - - - -
190B ASP* 5.5 4.5 - - + +
206B VAL* 3.3 31.9 - - + +
207B CYS* 3.3 25.4 + - - -
225B TRP* 3.5 22.4 - - + +
270B VAL* 2.9 23.9 + - + +
273B GLU* 1.3 74.2 - - + +
275B HIS* 1.3 58.3 + - - +
276B THR 3.0 1.6 - - - -
277B PHE* 3.0 1.0 + - - -
278B PHE* 2.7 51.2 + + + +
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Residues in contact with HIS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B TRP* 2.9 53.3 + + + -
226B PRO* 5.1 1.0 + - + +
228B VAL* 3.0 36.8 + - + -
229B LEU 5.6 2.5 - - - -
231B ILE* 4.2 8.5 - - + -
271B CYS 3.0 18.5 + - - +
272B VAL* 3.9 4.0 - - - +
274B HIS* 1.3 76.3 - - - +
276B THR* 1.3 63.3 + - - +
278B PHE 3.3 2.1 - - - +
279B ARG* 3.1 34.8 + - + +
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Residues in contact with THR 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B VAL* 2.8 29.1 + - - +
273B GLU* 3.8 5.4 - - - +
274B HIS 3.0 0.4 - - - -
275B HIS* 1.3 82.8 + - - +
277B PHE* 1.3 63.7 + - - +
278B PHE 3.5 0.2 + - - -
279B ARG* 3.8 20.4 - - - +
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Residues in contact with PHE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B TYR* 3.8 25.1 - + + -
42B PHE* 3.9 31.4 - + - -
79B PHE* 3.5 49.1 - + + -
273B GLU 2.9 19.3 + - - +
274B HIS* 3.0 2.4 + - - +
276B THR* 1.3 77.8 - - - +
278B PHE* 1.3 94.1 + + - +
279B ARG* 3.6 6.9 + - - -
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Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 5.7 0.4 - + - -
79B PHE* 3.9 16.2 - + + -
80B TYR 4.0 12.1 - - - -
81B PRO* 5.3 0.4 - - + -
82B PRO* 4.4 17.3 - - + -
208B SER* 3.4 46.0 - - - +
225B TRP* 3.8 24.2 - - + +
226B PRO* 4.7 3.1 - - - +
274B HIS* 2.7 39.9 + + - +
275B HIS 3.3 6.5 - - - +
277B PHE* 1.3 115.8 - + - +
279B ARG* 1.3 63.9 + - - +
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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
------------------------------------------------------------
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