Contacts of the helix formed by residues 297 - 308 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163L GLY 4.9 0.2 + - - -
165L SER* 3.9 7.6 + - - -
248L GLU* 3.3 21.8 - - - -
264L GLY* 3.9 12.6 - - - +
295L LEU* 3.3 7.4 - - - +
296L ASN* 1.4 86.2 + - - +
298L PHE* 1.3 62.3 + - - +
299L ALA* 3.4 7.4 + - - +
300L GLU* 3.0 26.1 + - - +
301L LEU* 3.3 18.5 + - - +
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Residues in contact with PHE 298 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244L ILE* 4.5 18.8 - - + -
246L GLY* 3.7 39.5 - - - -
247L THR* 3.9 15.7 - - - +
248L GLU* 2.8 22.7 + - + +
264L GLY 3.4 12.9 + - - +
265L ALA* 3.3 23.3 - - + -
297L SER* 1.3 71.0 - - - +
299L ALA* 1.3 55.9 + - + +
301L LEU* 3.2 17.3 + - + +
302L ARG* 2.8 55.7 + - + +
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Residues in contact with ALA 299 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165L SER* 3.6 25.6 - - - -
166L GLY 5.2 1.1 - - - +
173L GLU 4.1 1.4 - - - +
248L GLU* 3.1 13.1 + - - +
297L SER* 3.6 8.3 - - - +
298L PHE* 1.3 77.0 - - - +
300L GLU* 1.4 58.8 + - - +
302L ARG* 3.5 18.5 + - - +
303L SER* 3.0 29.8 + - - -
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Residues in contact with GLU 300 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L GLY* 4.9 1.1 - - - +
165L SER* 4.1 6.2 + - - +
173L GLU 4.7 0.2 - - - -
174L ASN* 3.3 25.7 + - - +
293L LYS* 4.7 4.5 - - - +
294L PRO 4.3 8.0 - - - +
295L LEU* 3.7 11.1 - - + +
296L ASN* 2.8 47.8 + - - +
297L SER* 3.0 22.1 + - - +
299L ALA* 1.4 71.4 - - - +
301L LEU* 1.3 60.0 + - - +
303L SER* 3.3 7.6 + - - -
304L ARG* 3.0 67.6 + - - +
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Residues in contact with LEU 301 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L LEU* 3.7 24.9 - - + -
244L ILE* 5.2 2.2 - - + -
265L ALA* 4.4 11.0 - - + -
287L ILE* 4.3 20.9 - - + -
290L LEU* 4.0 19.3 - - + -
295L LEU* 3.7 31.8 - - + +
297L SER 3.3 8.8 + - - +
298L PHE* 3.2 23.3 + - + +
300L GLU* 1.3 77.9 - - - +
302L ARG* 1.3 56.7 + - - +
304L ARG* 3.4 1.9 + - - +
305L ILE* 3.0 55.3 + - + +
316L LEU* 5.1 0.9 - - + -
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Residues in contact with ARG 302 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L GLN* 4.9 4.9 + - - -
171L GLY* 3.0 31.9 + - - -
172L LEU* 3.9 21.5 - - + +
173L GLU 5.3 1.0 - - - +
298L PHE* 2.8 44.8 + - + +
299L ALA* 3.5 20.1 + - - +
301L LEU* 1.3 75.0 - - - +
303L SER* 1.3 56.6 + - - +
305L ILE* 4.1 2.8 - - - +
306L ALA* 3.1 30.4 + - + +
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Residues in contact with SER 303 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172L LEU* 3.9 18.4 - - - +
173L GLU 3.4 32.4 + - - -
174L ASN* 3.3 24.8 - - - +
223L MET* 3.6 6.9 - - - +
299L ALA 3.0 10.0 + - - -
300L GLU 3.3 8.5 + - - -
301L LEU 3.4 0.2 - - - -
302L ARG* 1.3 74.3 - - - +
304L ARG* 1.3 66.2 + - - +
306L ALA* 3.6 1.9 + - - +
307L THR* 3.2 27.7 + - - -
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Residues in contact with ARG 304 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133L ASP* 2.6 37.8 + - - -
174L ASN* 4.0 21.7 + - - +
222L ASN* 5.9 2.8 - - - +
223L MET* 4.7 5.8 - - + -
290L LEU* 3.7 30.3 - - + +
293L LYS* 3.5 27.6 - - - +
295L LEU* 4.6 5.3 - - - +
300L GLU* 3.0 41.8 + - - +
301L LEU 3.9 1.1 - - - +
303L SER* 1.3 79.0 + - - +
305L ILE* 1.3 56.3 + - - +
307L THR* 3.4 8.5 + - - +
308L THR* 2.6 34.1 + - - +
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Residues in contact with ILE 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240L GLY* 3.5 7.9 - - - +
241L LEU* 3.8 12.1 - - - -
242L LEU* 3.8 55.0 - - + +
290L LEU* 3.9 28.7 - - + -
301L LEU* 3.0 35.2 + - + +
302L ARG* 4.3 3.4 - - - +
304L ARG* 1.3 73.2 - - - +
306L ALA* 1.3 62.4 + - - +
308L THR* 3.3 22.9 + - - +
314L VAL* 4.0 13.2 - - + -
331L LEU* 4.0 9.4 - - + +
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Residues in contact with ALA 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172L LEU* 3.7 29.6 - - + -
230L GLN* 4.9 0.2 + - - -
238L LYS 4.0 0.9 - - - +
239L ARG* 2.8 48.9 + - + +
240L GLY 3.6 12.6 + - - +
302L ARG 3.1 20.6 + - - +
303L SER 3.9 1.1 - - - +
304L ARG 3.4 0.2 - - - -
305L ILE* 1.3 76.9 - - - +
307L THR* 1.3 59.1 + - - +
308L THR 3.4 0.2 - - - -
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Residues in contact with THR 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L SER* 5.0 0.5 - - - -
172L LEU* 4.7 5.4 - - - +
223L MET* 3.7 46.8 - - + +
226L THR* 3.4 26.5 - - + +
227L LEU* 4.1 15.0 - - + +
230L GLN* 3.5 13.0 + - - +
239L ARG* 4.4 7.9 + - - +
303L SER 3.2 18.5 + - - -
304L ARG* 3.7 7.9 - - - +
305L ILE 3.2 0.2 - - - -
306L ALA* 1.3 74.7 - - - +
308L THR* 1.3 63.5 + - - +
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Residues in contact with THR 308 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L THR* 4.9 5.4 - - + -
238L LYS 3.6 1.7 - - - +
240L GLY* 3.1 26.0 + - - -
290L LEU* 5.8 1.4 - - - +
304L ARG 2.6 24.1 + - - -
305L ILE* 3.3 6.5 + - - +
307L THR* 1.3 78.6 - - - +
309L GLU* 1.3 64.4 + - - +
312L THR* 3.7 29.4 - - + +
314L VAL* 4.6 8.9 - - + +
331L LEU* 3.7 21.0 - - + +
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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