Contacts of the helix formed by residues 297 - 308 (chain I) in PDB entry 3STJ
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 297 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163I GLY 4.9 0.2 + - - -
165I SER* 4.1 6.5 + - - -
248I GLU* 3.3 21.5 - - - -
264I GLY 3.9 12.3 - - - +
295I LEU* 3.3 9.4 - - - +
296I ASN* 1.4 87.5 + - - +
298I PHE* 1.3 62.5 + - - +
299I ALA* 3.5 6.7 + - - +
300I GLU* 3.0 26.9 + - - +
301I LEU* 3.4 17.5 + - - +
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Residues in contact with PHE 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I ILE* 4.4 19.1 - - + -
246I GLY* 3.7 37.2 - - - -
247I THR* 3.8 20.2 - - - +
248I GLU* 2.9 23.5 + - + +
264I GLY 3.5 7.8 + - - +
265I ALA* 3.3 25.4 - - + -
297I SER* 1.3 69.9 - - - +
299I ALA* 1.4 57.4 + - - +
301I LEU* 3.1 16.0 + - + +
302I ARG* 2.8 55.6 + - + +
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Residues in contact with ALA 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165I SER* 3.6 27.8 - - - -
166I GLY* 5.1 2.2 - - - +
173I GLU 4.1 1.0 - - - +
248I GLU* 3.1 13.5 + - - +
297I SER* 3.7 5.2 - - - +
298I PHE* 1.4 77.3 - - - +
300I GLU* 1.4 58.7 + - - +
302I ARG* 3.6 14.7 + - - +
303I SER* 3.0 29.6 + - - -
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Residues in contact with GLU 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163I GLY* 4.8 1.0 - - - -
165I SER* 3.9 6.0 + - - +
174I ASN* 3.3 24.4 + - - +
293I LYS* 4.7 4.5 - - - +
294I PRO 4.3 8.4 - - - +
295I LEU* 3.7 10.4 - - + +
296I ASN* 2.8 49.6 + - - +
297I SER* 3.0 22.8 + - - +
298I PHE 3.3 0.2 - - - -
299I ALA* 1.4 71.2 - - - +
301I LEU* 1.3 60.4 + - - +
303I SER* 2.8 20.3 + - - -
304I ARG* 2.9 54.2 + - - +
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Residues in contact with LEU 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242I LEU* 3.8 24.7 - - + -
244I ILE* 5.2 2.0 - - + -
265I ALA* 4.3 11.0 - - + -
287I ILE* 4.3 21.8 - - + -
290I LEU* 3.9 21.3 - - + -
295I LEU* 3.7 29.5 - - + +
297I SER 3.4 10.3 + - - +
298I PHE* 3.1 23.3 + - + +
300I GLU* 1.3 76.5 - - - +
302I ARG* 1.3 63.1 + - - +
304I ARG* 3.3 2.6 + - - +
305I ILE* 3.0 46.5 + - + +
316I LEU* 5.1 0.9 - - + -
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Residues in contact with ARG 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I GLN* 4.6 7.9 + - - -
171I GLY* 3.0 29.5 + - - -
172I LEU* 3.9 19.0 - - + +
173I GLU 5.6 0.4 - - - +
298I PHE* 2.8 42.6 + - + +
299I ALA* 3.6 14.7 + - - +
301I LEU* 1.3 74.9 - - - +
303I SER* 1.3 57.4 + - - +
305I ILE* 3.5 3.2 + - - +
306I ALA* 3.1 33.3 + - + +
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Residues in contact with SER 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172I LEU* 3.9 20.5 - - - +
173I GLU 3.2 37.7 + - - -
174I ASN* 3.5 12.0 - - - +
223I MET* 3.8 7.9 - - - +
299I ALA 3.0 12.7 + - - -
300I GLU 2.8 18.5 + - - -
302I ARG* 1.3 75.5 - - - +
304I ARG* 1.4 57.4 + - - +
306I ALA* 4.0 1.4 + - - +
307I THR* 3.2 29.8 + - - -
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Residues in contact with ARG 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I ASP* 2.7 39.1 + - - -
174I ASN* 3.7 24.9 + - - +
222I ASN* 6.2 0.6 - - - +
223I MET* 4.7 5.6 - - + -
290I LEU* 3.7 30.8 + - + +
293I LYS* 3.6 22.0 - - - +
295I LEU* 4.5 6.0 - - - +
300I GLU* 2.9 48.7 + - - +
301I LEU 3.8 1.8 - - - +
303I SER* 1.4 75.0 + - - +
305I ILE* 1.3 57.0 - - - +
307I THR* 3.7 6.6 + - - +
308I THR* 2.6 32.3 + - - -
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Residues in contact with ILE 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240I GLY* 3.5 19.7 - - - +
241I LEU* 3.8 17.3 - - - -
242I LEU* 3.8 23.1 - - + +
290I LEU* 3.9 30.1 - - + -
301I LEU* 3.0 32.8 + - + +
302I ARG* 4.1 3.1 - - - +
304I ARG* 1.3 71.9 - - - +
306I ALA* 1.3 57.4 + - - +
307I THR 3.1 1.6 - - - -
308I THR* 2.8 33.2 + - - +
314I VAL* 4.0 22.4 - - + -
331I LEU* 4.1 14.3 - - + +
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Residues in contact with ALA 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172I LEU* 3.8 30.3 - - + -
238I LYS 4.0 1.6 - - - +
239I ARG* 3.0 45.5 + - + +
240I GLY 3.5 14.3 + - - +
302I ARG* 3.1 19.6 + - + +
303I SER 4.2 0.4 - - - +
305I ILE* 1.3 74.6 - - - +
307I THR* 1.3 60.2 + - - +
308I THR 3.8 0.2 - - - +
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Residues in contact with THR 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I SER* 5.1 0.5 - - - -
172I LEU* 4.6 5.9 - - - +
223I MET* 3.7 50.2 - - + +
226I THR* 3.4 13.4 - - + +
227I LEU* 4.0 19.7 - - + +
230I GLN* 3.3 22.9 + - - +
238I LYS 5.0 0.9 - - - -
239I ARG* 4.5 3.2 + - - +
303I SER 3.2 19.3 + - - -
304I ARG* 3.8 6.7 - - - +
305I ILE 3.1 0.4 - - - -
306I ALA* 1.3 74.6 - - - +
308I THR* 1.4 60.3 + - - +
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Residues in contact with THR 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I THR* 4.8 5.8 - - + +
238I LYS 3.7 1.7 - - - +
240I GLY* 3.2 19.4 + - - -
290I LEU* 5.9 0.7 - - - +
304I ARG 2.6 21.9 + - - -
305I ILE* 2.8 21.2 + - - +
307I THR* 1.4 78.8 - - - +
309I GLU* 1.3 64.8 + - - +
312I THR* 3.7 32.1 - - + +
314I VAL* 4.6 8.4 - - + +
331I LEU* 3.7 13.7 - - + -
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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