Contacts of the helix formed by residues 297 - 308 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163J GLY 4.8 0.5 + - - -
165J SER* 4.2 6.2 + - - -
248J GLU* 3.3 21.5 - - - -
264J GLY* 3.9 12.1 - - - +
295J LEU* 3.3 11.9 + - - +
296J ASN* 1.3 88.5 + - - +
298J PHE* 1.3 61.7 + - - +
299J ALA* 3.5 6.4 + - - +
300J GLU* 2.9 27.1 + - - +
301J LEU* 3.4 15.1 + - - +
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Residues in contact with PHE 298 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244J ILE* 4.5 18.4 - - + -
245J LYS* 5.2 0.4 - - - -
246J GLY* 3.7 38.4 - - - -
247J THR* 3.8 20.0 - - - +
248J GLU* 2.9 24.0 + - + +
264J GLY 3.5 7.2 + - - +
265J ALA* 3.3 27.6 - - + -
297J SER* 1.3 70.3 - - - +
299J ALA* 1.4 55.8 + - - +
301J LEU* 3.2 15.7 + - + +
302J ARG* 2.7 54.5 + - + +
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Residues in contact with ALA 299 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165J SER* 3.5 29.4 - - - -
166J GLY 5.1 1.6 - - - +
173J GLU 4.1 1.7 - - - +
248J GLU* 3.1 12.7 + - - +
297J SER* 3.6 5.4 - - - +
298J PHE* 1.4 76.6 - - + +
300J GLU* 1.3 58.7 + - - +
302J ARG* 3.6 13.5 + - - +
303J SER* 3.0 29.5 + - - -
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Residues in contact with GLU 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163J GLY* 4.9 0.7 - - - +
165J SER* 4.0 6.2 + - - +
174J ASN* 3.3 23.6 - - - +
293J LYS* 4.7 3.1 - - - +
294J PRO 4.3 8.1 - - - +
295J LEU* 3.7 11.8 - - + +
296J ASN* 2.8 47.9 + - - +
297J SER* 2.9 21.9 + - - +
299J ALA* 1.3 72.4 - - - +
301J LEU* 1.4 54.3 + - - +
303J SER* 3.0 8.3 + - - -
304J ARG* 2.8 74.8 + - - +
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Residues in contact with LEU 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242J LEU* 3.7 26.0 - - + -
244J ILE* 5.4 2.5 - - + -
265J ALA* 3.8 17.5 - - + -
287J ILE* 3.6 26.7 - - + -
290J LEU* 5.2 3.6 - - + -
295J LEU* 3.6 38.7 - - + +
297J SER 3.4 5.8 + - - +
298J PHE* 3.2 23.5 + - + +
300J GLU* 1.4 76.9 - - - +
302J ARG* 1.3 68.8 + - - +
304J ARG* 3.1 5.2 + - - +
305J ILE* 2.9 39.3 + - + +
316J LEU* 5.8 0.9 - - + -
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Residues in contact with ARG 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J GLN* 4.6 7.3 + - - -
171J GLY* 3.0 30.3 + - - -
172J LEU* 3.9 19.4 - - + +
173J GLU 5.7 0.4 - - - +
298J PHE* 2.7 42.1 + - + +
299J ALA* 3.6 14.3 + - - +
301J LEU* 1.3 78.7 - - - +
303J SER* 1.3 57.3 + - - +
305J ILE* 3.3 3.9 + - - +
306J ALA* 3.0 30.7 + - + +
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Residues in contact with SER 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172J LEU* 3.9 21.3 - - - +
173J GLU 3.3 36.4 + - - -
174J ASN* 3.4 14.6 - - - +
223J MET* 3.9 5.7 - - - +
299J ALA 3.0 14.7 + - - -
300J GLU 3.0 10.2 + - - -
302J ARG* 1.3 77.1 - - - +
304J ARG* 1.3 62.9 + - - +
306J ALA* 3.6 1.7 + - - +
307J THR* 3.3 27.7 + - - -
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Residues in contact with ARG 304 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J ASP* 2.8 35.3 + - - -
163J GLY* 5.8 0.8 - - - -
174J ASN* 3.3 26.4 + - - +
222J ASN* 5.9 2.6 - - - +
223J MET* 4.8 5.2 - - + -
290J LEU* 3.7 28.4 - - + +
293J LYS* 3.9 17.6 - - - +
295J LEU* 4.7 5.1 - - - +
300J GLU* 2.8 56.7 + - - +
301J LEU 3.7 3.1 - - - +
303J SER* 1.3 72.9 + - - +
305J ILE* 1.3 54.5 + - - +
307J THR* 3.9 8.7 + - + +
308J THR* 2.6 32.6 + - - -
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Residues in contact with ILE 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240J GLY* 3.5 16.3 - - - +
241J LEU* 3.9 2.7 - - - -
242J LEU* 3.8 44.4 - - + +
290J LEU* 3.8 33.9 - - + -
301J LEU* 2.9 40.5 + - + +
302J ARG* 3.9 3.8 - - - +
304J ARG* 1.3 72.9 - - - +
306J ALA* 1.3 56.9 + - - +
307J THR 3.1 4.9 - - - -
308J THR* 3.1 28.9 + - - +
314J VAL* 4.5 10.1 - - + -
331J LEU* 4.0 11.6 - - + +
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Residues in contact with ALA 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172J LEU* 3.8 25.4 - - + -
238J LYS 4.2 1.4 - - - +
239J ARG* 2.7 54.8 + - + +
240J GLY 3.6 12.8 + - - +
302J ARG* 3.0 17.8 + - + +
303J SER 4.1 0.9 - - - +
304J ARG 3.6 0.2 - - - -
305J ILE* 1.3 75.9 - - - +
307J THR* 1.3 58.6 + - - +
308J THR 4.2 1.1 - - - -
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Residues in contact with THR 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J SER* 5.2 0.5 - - - -
172J LEU* 5.1 4.5 - - - +
223J MET* 3.4 45.0 - - + +
226J THR* 3.4 20.2 - - + +
227J LEU* 4.0 19.3 - - + +
230J GLN* 3.0 24.4 + - - +
238J LYS 5.1 0.4 - - - -
239J ARG* 4.5 2.0 + - - +
303J SER 3.3 18.0 + - - -
304J ARG* 3.9 9.2 - - - +
305J ILE 3.1 0.2 - - - -
306J ALA* 1.3 74.5 - - - +
308J THR* 1.4 64.3 + - - +
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Residues in contact with THR 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226J THR* 4.7 5.8 - - + +
238J LYS 3.7 1.8 - - - +
240J GLY* 3.2 26.7 + - - -
290J LEU* 5.9 0.9 - - - +
304J ARG 2.6 22.3 + - - -
305J ILE* 3.1 13.9 + - - +
307J THR* 1.4 81.1 - - - +
309J GLU* 1.3 65.0 + - - +
312J THR* 3.7 32.3 - - + +
314J VAL* 4.6 9.4 - - + +
331J LEU* 3.7 12.6 - - + -
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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