Contacts of the helix formed by residues 304 - 319 (chain C) in PDB entry 4NQJ
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 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A HIS* 3.5 11.7 - - - -
206A GLU* 5.0 1.3 - - - -
299C LEU* 4.5 8.3 - - - -
302C TYR* 3.0 6.5 - - - +
303C LYS* 1.3 82.0 - - - +
305C PRO* 1.3 69.9 - - - +
306C ILE 3.4 2.5 - - - -
307C GLN* 3.4 10.1 - - - +
308C TYR* 3.1 28.4 + - - +
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Residues in contact with PRO 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A HIS* 4.4 2.2 - - + -
203A VAL* 3.8 39.0 - - + +
206A GLU* 3.8 24.0 - - + -
207A PHE* 3.4 33.2 - - + -
221C ILE* 3.9 11.2 - - + +
299C LEU* 4.6 4.9 - - + -
304C GLY* 1.3 84.8 - - - +
306C ILE* 1.3 62.5 + - + +
308C TYR* 3.4 7.9 - - + +
309C MET* 2.8 34.1 + - - +
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Residues in contact with ILE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU* 4.7 17.0 - - + +
207A PHE* 5.2 2.2 - - + -
210A LEU* 4.1 25.4 - - + -
402A LMT 3.9 39.0 - - + +
304C GLY 3.4 0.8 - - - -
305C PRO* 1.3 83.3 - - + +
307C GLN* 1.3 79.8 + - - +
309C MET* 3.2 22.3 + - + +
310C VAL* 3.0 42.8 + - + +
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Residues in contact with GLN 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU* 4.2 11.1 - - - +
317B THR* 3.5 17.6 + - + +
318B LEU* 3.4 32.8 - - + +
302C TYR* 4.8 1.3 - - - -
303C LYS* 3.6 29.1 - - + +
304C GLY* 3.4 37.1 - - - +
306C ILE* 1.3 87.6 + - - +
308C TYR* 1.3 64.7 + - - +
310C VAL* 3.4 7.8 + - - +
311C TRP* 3.0 24.1 + - - +
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Residues in contact with TYR 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ILE* 4.1 26.9 - - + -
224C GLU* 2.2 35.1 + - - -
298C ASN* 6.1 3.4 - - + -
299C LEU* 4.2 19.7 - - + -
302C TYR* 3.8 47.0 - + + -
304C GLY 3.1 20.0 + - - +
305C PRO* 3.4 10.1 - - + +
307C GLN* 1.3 78.0 - - - +
309C MET* 1.3 60.6 + - + +
311C TRP* 3.3 2.3 + - - +
312C ARG* 2.9 70.5 + - + +
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Residues in contact with MET 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PHE* 3.6 27.4 - - + -
210A LEU* 5.1 0.9 - - + -
213C PHE* 5.3 3.8 - - - -
214C LEU* 4.4 13.2 - - + -
217C LYS* 3.4 38.6 - - + +
221C ILE* 3.8 13.9 - - + -
305C PRO 2.8 18.1 + - - +
306C ILE* 3.2 32.3 + - + +
308C TYR* 1.3 76.5 - - + +
310C VAL* 1.3 64.3 + - + +
312C ARG* 3.3 3.2 + - - -
313C GLU* 3.0 39.2 + - + +
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Residues in contact with VAL 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LMT 4.8 15.9 - - + -
318B LEU* 4.9 6.1 - - + -
306C ILE* 3.0 31.3 + - + +
307C GLN* 3.6 10.5 - - - +
309C MET* 1.3 76.3 - - + +
311C TRP* 1.3 64.2 + - - +
313C GLU* 3.0 17.9 + - - +
314C MET* 3.1 39.0 + - + +
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Residues in contact with TRP 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B TRP* 5.4 15.7 - + - -
318B LEU* 3.7 33.6 - - + +
302C TYR* 3.4 39.0 + + + -
307C GLN 3.0 18.1 + - - +
308C TYR 3.5 3.6 - - - +
310C VAL* 1.3 74.4 - - - +
312C ARG* 1.3 66.2 + - + +
314C MET* 3.2 21.6 + - + +
315C GLN* 2.9 52.7 + - + +
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Residues in contact with ARG 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C GLU* 4.5 10.5 + - - -
302C TYR* 6.0 0.2 - - - -
308C TYR* 2.9 62.2 + - + +
309C MET* 3.8 5.6 - - - +
311C TRP* 1.3 80.2 - - + +
313C GLU* 1.3 64.5 + - - +
315C GLN* 3.2 30.8 + - - +
316C ASP* 2.6 77.9 + - - +
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Residues in contact with GLU 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LYS* 4.9 16.8 + - - -
309C MET* 3.0 38.3 + - + +
310C VAL* 3.0 9.6 + - - +
312C ARG* 1.3 82.8 - - - +
314C MET* 1.3 65.2 + - + +
316C ASP* 3.2 12.1 + - - +
317C THR* 3.2 30.3 + - + +
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Residues in contact with MET 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B MET* 6.3 2.5 - - + -
318B LEU* 5.1 5.8 - - + -
310C VAL* 3.1 35.7 + - + +
311C TRP* 3.4 27.6 - - + +
313C GLU* 1.3 77.2 - - + +
315C GLN* 1.3 62.4 + - - +
317C THR* 3.0 22.8 + - - -
318C LEU* 3.3 18.7 + - + +
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Residues in contact with GLN 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C TYR* 5.3 0.8 + - - -
311C TRP* 2.9 43.6 + - + +
312C ARG* 3.2 39.6 + - - +
314C MET* 1.3 76.9 - - - +
316C ASP* 1.3 57.8 + - - +
318C LEU* 3.4 2.1 + - - -
319C CYS* 2.8 53.1 + - + +
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Residues in contact with ASP 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C ARG* 2.6 58.1 + - - +
313C GLU* 3.2 14.7 + - - +
314C MET 3.2 0.8 - - - -
315C GLN* 1.3 82.6 - - - +
317C THR* 1.3 60.9 + - + +
319C CYS 3.5 14.7 - - - +
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Residues in contact with THR 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C GLU* 3.2 15.6 + - + +
314C MET* 3.0 18.3 + - - -
316C ASP* 1.3 79.9 - - + +
318C LEU* 1.3 73.8 + - - +
319C CYS 4.7 0.4 - - - +
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C MET* 3.3 20.2 + - + +
315C GLN* 4.2 2.5 - - - +
317C THR* 1.3 92.2 + - - +
319C CYS* 1.3 66.8 + - - +
320C PRO* 4.5 2.4 - - - +
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Residues in contact with CYS 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C GLN* 2.8 31.6 + - + +
316C ASP* 3.5 19.1 - - - +
317C THR 4.7 0.5 - - - -
318C LEU* 1.3 90.7 - - - +
320C PRO* 1.3 75.8 - - + +
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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