Contacts of the helix formed by residues 297 - 308 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLY 4.8 0.2 + - - -
165B SER* 4.4 6.6 + - - -
248B GLU* 3.3 22.0 - - - -
264B GLY 3.9 11.1 - - - +
295B LEU* 3.3 11.1 + - - +
296B ASN* 1.4 88.6 + - - +
298B PHE* 1.3 61.5 + - - +
299B ALA* 3.5 7.5 + - - +
300B GLU* 3.0 26.7 + - - +
301B LEU* 3.4 15.4 + - - +
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Residues in contact with PHE 298 (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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244B ILE* 4.4 19.7 - - + -
245B LYS* 5.4 0.2 - - - -
246B GLY* 3.7 37.2 - - - -
247B THR* 3.9 15.9 - - - +
248B GLU* 2.9 24.2 + - + +
264B GLY 3.5 11.5 + - - +
265B ALA* 3.3 24.2 - - + -
297B SER* 1.3 70.6 - - - +
299B ALA* 1.3 56.2 + - - +
301B LEU* 3.2 16.4 + - + +
302B ARG* 2.8 56.0 + - + +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B SER* 3.6 28.3 - - - -
166B GLY* 5.1 2.0 - - - +
173B GLU 4.1 2.4 + - - +
248B GLU* 3.1 12.9 + - - +
297B SER* 3.3 5.6 - - - +
298B PHE* 1.3 80.8 - - + +
300B GLU* 1.4 56.1 + - - +
302B ARG* 3.5 14.7 + - - +
303B SER* 3.1 28.2 + - - -
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Residues in contact with GLU 300 (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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163B GLY* 4.8 2.4 - - - +
165B SER* 4.1 5.3 + - - +
174B ASN* 3.3 24.9 + - - +
293B LYS* 4.7 4.9 - - - +
294B PRO 4.3 7.7 - - - +
295B LEU* 3.7 10.7 - - + +
296B ASN* 2.8 48.9 + - - +
297B SER* 3.0 21.8 + - - +
298B PHE 3.3 0.2 - - - -
299B ALA* 1.4 71.9 - - - +
301B LEU* 1.3 60.1 + - - +
303B SER* 3.0 7.5 + - - -
304B ARG* 2.9 67.8 + - - +
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Residues in contact with LEU 301 (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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242B LEU* 3.7 24.0 - - + -
244B ILE* 5.2 2.0 - - + -
265B ALA* 4.4 10.3 - - + -
287B ILE* 4.3 16.4 - - + -
290B LEU* 4.0 16.4 - - + -
295B LEU* 3.7 32.0 - - + +
297B SER 3.4 10.1 + - - +
298B PHE* 3.2 22.4 + - + +
300B GLU* 1.3 78.6 - - - +
302B ARG* 1.3 57.0 - - - +
304B ARG* 3.3 2.5 + - - -
305B ILE* 2.9 56.9 + - + +
316B LEU* 4.7 4.7 - - + -
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLN* 4.6 7.5 + - - -
171B GLY* 3.0 29.9 + - - -
172B LEU* 3.9 18.4 - - + +
173B GLU 5.7 0.2 - - - +
298B PHE* 2.8 42.0 + - + +
299B ALA* 3.6 15.0 + - - +
301B LEU* 1.3 75.8 - - - +
303B SER* 1.3 56.2 + - - +
305B ILE* 3.9 4.1 - - - +
306B ALA* 3.0 32.1 + - + +
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 4.0 18.9 - - - +
173B GLU 3.5 32.8 + - - -
174B ASN* 3.3 22.0 - - - +
223B MET* 3.8 6.1 - - - +
299B ALA 3.1 9.7 + - - -
300B GLU 3.0 11.1 + - - -
302B ARG* 1.3 74.1 - - - +
304B ARG* 1.3 66.2 + - - +
306B ALA* 3.6 0.9 + - - +
307B THR* 2.9 31.0 + - - -
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Residues in contact with ARG 304 (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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133B ASP* 2.7 38.8 + - - -
174B ASN* 3.7 24.4 + - - +
222B ASN* 6.0 2.0 - - - +
223B MET* 4.7 5.8 - - + -
290B LEU* 3.6 30.9 - - + +
293B LYS* 3.6 20.6 - - - +
295B LEU* 4.5 6.0 - - - +
300B GLU* 2.9 48.6 + - - +
301B LEU 3.8 0.9 - - - +
303B SER* 1.3 79.0 + - - +
305B ILE* 1.3 55.9 + - - +
307B THR* 3.6 7.2 + - - +
308B THR* 2.6 32.2 + - - -
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Residues in contact with ILE 305 (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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240B GLY* 3.4 17.4 - - - +
241B LEU* 3.9 2.2 - - - -
242B LEU* 3.8 47.3 - - + +
290B LEU* 3.8 31.6 - - + -
301B LEU* 2.9 35.6 + - + +
302B ARG* 4.1 4.0 - - - +
304B ARG* 1.3 75.6 - - - +
306B ALA* 1.3 60.7 + - - +
308B THR* 3.2 23.8 + - - +
314B VAL* 4.1 13.5 - - + -
331B LEU* 3.9 13.1 - - + +
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Residues in contact with ALA 306 (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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172B LEU* 3.8 23.6 - - + -
230B GLN* 5.4 0.2 + - - -
238B LYS 4.3 1.2 - - - +
239B ARG* 2.7 55.6 + - + +
240B GLY 3.6 12.4 + - - +
302B ARG* 3.0 18.8 + - + +
303B SER 4.2 0.7 - - - +
304B ARG 3.5 0.2 - - - -
305B ILE* 1.3 76.9 - - - +
307B THR* 1.3 58.8 + - - +
308B THR 4.0 0.8 - - - +
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Residues in contact with THR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER* 5.2 0.5 - - - -
172B LEU* 4.7 5.5 - - - +
222B ASN 5.6 0.2 - - - -
223B MET* 3.7 54.3 - - + +
226B THR* 3.4 14.0 - - + +
227B LEU* 4.2 20.0 - - + +
230B GLN* 3.0 23.1 - - - +
239B ARG* 4.3 2.5 + - - +
303B SER 2.9 21.0 + - - -
304B ARG* 3.7 7.0 - - - +
306B ALA* 1.3 73.2 - - - +
308B THR* 1.3 61.0 + - - +
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Residues in contact with THR 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 4.8 7.4 - - + +
238B LYS 3.7 2.0 - - - +
240B GLY* 3.2 26.3 + - - -
290B LEU* 6.0 0.7 - - - +
304B ARG 2.6 21.8 + - - -
305B ILE* 3.2 14.0 + - - +
307B THR* 1.3 82.0 - - - +
309B GLU* 1.4 65.0 + - - +
312B THR* 3.7 32.5 - - + +
314B VAL* 4.6 9.0 - - + +
331B LEU* 3.7 13.6 - - + +
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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