Contacts of the helix formed by residues 258 - 268 (chain A) in PDB entry 1SQG
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 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A ALA 2.6 23.0 + - - -
256A ALA* 3.5 0.2 - - - +
257A PRO* 1.3 73.9 - - - +
259A GLY* 1.3 64.0 + - - +
260A LYS 3.4 2.0 - - - -
261A THR* 3.4 16.9 - - - -
262A THR* 3.2 28.4 + - - +
286A VAL* 4.1 13.5 - - - -
289A ASN* 4.0 8.3 - - - +
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Residues in contact with GLY 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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177A ARG* 2.8 26.4 + - - -
229A THR* 5.0 8.3 - - - -
230A VAL 6.1 0.2 - - - -
231A GLN* 3.5 16.6 - - - -
255A ALA 4.4 0.6 + - - -
257A PRO* 3.5 12.4 - - - +
258A GLY* 1.3 78.5 - - - +
260A LYS* 1.3 59.4 + - - +
262A THR* 3.1 11.6 + - - -
263A HIS* 3.2 2.8 + - - +
289A ASN* 4.3 4.0 - - - +
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Residues in contact with LYS 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLN* 3.9 16.4 - - - +
235A ALA* 4.7 11.0 - - + +
238A CYS* 4.1 19.1 - - + -
239A MET* 4.0 3.8 - - + +
252A ASP* 3.5 17.1 + - - +
253A LEU 5.1 0.2 + - - -
254A CYS 3.9 10.7 + - - -
255A ALA 4.5 6.7 + - - -
256A ALA 5.4 1.2 + - - -
258A GLY* 3.4 0.4 - - - -
259A GLY* 1.3 74.8 - - - +
261A THR* 1.3 66.3 + - - +
263A HIS* 3.2 7.2 + - - +
264A ILE* 3.0 29.5 + - - +
320A LEU* 3.3 39.7 - - + -
322A ASP* 2.8 43.3 + - - +
421A PHE* 5.6 0.4 - - + -
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Residues in contact with THR 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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252A ASP* 2.5 26.1 + - - +
255A ALA* 3.6 14.0 - - - +
258A GLY* 3.4 17.6 - - - -
260A LYS* 1.3 77.3 - - - +
262A THR* 1.3 63.3 + - - +
264A ILE* 3.4 19.8 + - - +
265A LEU* 3.5 11.4 + - + +
273A VAL* 4.2 16.3 - - + +
275A ALA* 3.9 19.8 - - + +
286A VAL* 4.5 4.9 - - + +
290A LEU* 4.2 19.3 - - + -
297A ALA* 4.8 5.6 - - + -
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Residues in contact with THR 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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177A ARG* 2.9 25.2 + - - -
229A THR* 4.9 1.7 + - - +
258A GLY 3.2 12.2 + - - +
259A GLY* 3.1 10.6 + - - -
261A THR* 1.3 74.8 - - - +
263A HIS* 1.3 59.2 + - - +
265A LEU* 3.1 1.8 + - - -
266A GLU* 2.9 31.0 + - - +
289A ASN* 3.7 32.3 + - + +
290A LEU* 3.9 15.3 - - + -
293A LEU* 3.9 7.7 - - + +
295A MET* 3.4 26.8 - - - +
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Residues in contact with HIS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG* 3.4 33.8 + - - +
180A ARG* 4.5 0.7 - - - -
207A ASP* 3.0 28.9 + - - -
231A GLN* 3.9 4.3 - - - -
235A ALA 4.8 0.7 - - - -
236A GLN* 3.4 33.7 + - - +
239A MET* 3.1 34.8 - - + +
259A GLY 3.2 15.3 + - - +
260A LYS* 3.2 11.6 + - - +
262A THR* 1.3 78.3 + - - +
264A ILE* 1.3 63.0 + - - +
266A GLU* 3.1 7.7 + - + +
267A VAL* 3.0 29.4 + - + +
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Residues in contact with ILE 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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239A MET* 3.7 24.0 - - + -
242A LEU* 3.8 18.2 - - + -
244A PRO* 3.7 22.8 - - + +
250A ILE* 4.3 15.5 - - + -
252A ASP* 4.2 20.9 - - + +
260A LYS 3.0 16.7 + - - +
261A THR* 3.4 15.5 - - - +
263A HIS* 1.3 77.6 - - - +
265A LEU* 1.3 52.5 + - - +
267A VAL* 3.3 3.1 + - - +
268A ALA* 2.7 32.7 + - - +
271A ALA* 4.4 6.3 - - + -
273A VAL* 3.8 25.1 - - + -
320A LEU* 4.6 1.1 - - + -
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Residues in contact with LEU 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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181A THR* 4.9 1.9 - - - +
261A THR* 3.5 12.3 + - + +
262A THR 3.1 2.3 + - - +
264A ILE* 1.3 75.4 - - - +
266A GLU* 1.3 63.1 + - - +
268A ALA 3.4 17.3 - - - +
269A PRO* 3.1 34.6 - - + +
271A ALA* 3.5 23.3 - - + +
273A VAL* 4.0 16.2 - - + -
290A LEU* 4.4 9.9 - - + -
295A MET* 3.5 44.7 - - + +
296A LYS 3.9 21.1 - - - +
297A ALA* 4.6 6.5 - - + -
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Residues in contact with GLU 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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177A ARG* 2.8 45.6 + - - +
178A ILE 3.9 3.5 - - - +
179A ASN* 3.2 49.3 + - - +
180A ARG* 3.6 27.9 + - + +
181A THR* 3.9 12.8 - - - +
207A ASP* 5.2 1.6 - - - +
228A VAL 6.2 0.2 - - - -
229A THR* 4.6 1.2 + - - -
262A THR 2.9 13.8 + - - +
263A HIS* 3.1 12.3 + - - +
265A LEU* 1.3 76.5 - - - +
267A VAL* 1.3 62.3 + - - +
269A PRO* 4.2 4.2 - - - +
293A LEU* 3.2 8.0 - - - +
295A MET* 3.7 11.0 - - + -
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ARG* 3.7 36.4 + - - +
239A MET* 4.0 24.7 - - + +
243A ALA* 5.4 1.1 - - - -
244A PRO* 3.9 30.9 - - + +
246A ASN* 5.5 0.9 + - - -
263A HIS* 3.0 17.3 + - - +
264A ILE 3.6 6.3 - - - +
266A GLU* 1.3 81.6 - - - +
268A ALA* 1.3 57.3 + - - +
269A PRO* 3.7 5.7 - - - +
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Residues in contact with ALA 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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244A PRO* 3.8 18.8 - - + +
245A GLN* 3.6 26.7 - - - +
246A ASN* 3.1 13.5 - - - +
264A ILE 2.7 13.9 + - - +
265A LEU* 3.4 11.6 - - - +
267A VAL* 1.3 74.6 - - - +
269A PRO* 1.3 70.1 - - - +
270A GLU 3.0 1.6 + - - -
271A ALA* 3.1 17.6 + - + +
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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
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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