Contacts of the helix formed by residues 304 - 319 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A LEU* 4.6 7.6 - - - -
302A TYR* 3.2 5.4 - - - +
303A LYS* 1.3 78.7 - - - +
305A PRO* 1.3 71.9 - - - +
307A GLN* 3.1 13.5 + - - +
308A TYR* 3.0 28.3 + - - +
202C HIS* 3.8 9.4 - - - -
206C GLU* 5.0 2.0 - - - -
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Residues in contact with PRO 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ILE* 4.1 8.2 - - + +
299A LEU* 4.7 4.7 - - + -
304A GLY* 1.3 82.2 - - - +
306A ILE* 1.3 62.1 + - + +
307A GLN* 4.7 0.4 - - - +
308A TYR* 3.5 7.5 - - + +
309A MET* 2.9 37.1 + - - +
202C HIS* 4.3 3.1 - - + -
203C VAL* 3.9 34.8 - - + +
206C GLU* 3.6 33.7 - - + -
207C PHE* 3.5 27.8 - - + -
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Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A GLY 3.3 0.4 - - - -
305A PRO* 1.3 81.0 - - + +
307A GLN* 1.3 78.0 - - + +
309A MET* 3.2 22.3 + - + +
310A VAL* 3.2 21.8 + - + +
206C GLU* 4.2 21.5 - - - +
207C PHE* 5.9 1.6 - - + -
210C LEU* 3.8 32.1 - - + -
401C LMT 3.9 57.6 - - + +
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Residues in contact with GLN 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 4.6 7.5 - - + -
303A LYS* 3.6 33.8 - - + +
304A GLY* 3.1 31.3 + - - +
306A ILE* 1.3 87.2 + - + +
308A TYR* 1.3 61.6 + - - +
310A VAL* 3.4 9.5 + - - +
311A TRP* 3.2 23.7 + - - +
206C GLU* 5.2 7.0 + - - +
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Residues in contact with TYR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ILE* 4.4 24.0 - - + -
224A GLU* 2.3 36.5 + - - -
298A ASN* 3.8 22.7 + - - -
299A LEU* 3.8 23.3 - - + -
302A TYR* 3.4 37.2 - + + -
304A GLY 3.0 19.0 + - - +
305A PRO 3.5 6.7 - - - +
306A ILE 3.1 0.2 - - - -
307A GLN* 1.3 77.8 - - - +
309A MET* 1.3 66.6 + - + +
311A TRP* 3.6 0.3 + - - +
312A ARG* 3.0 64.3 + - + +
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Residues in contact with MET 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 4.7 3.4 - - + -
217A LYS* 3.7 45.5 - - + +
221A ILE* 3.8 15.3 - - + -
305A PRO 2.9 20.0 + - - +
306A ILE* 3.6 15.9 - - + +
308A TYR* 1.3 80.2 - - + +
310A VAL* 1.3 63.2 + - - +
312A ARG* 3.9 4.0 - - - +
313A GLU* 3.0 24.1 + - - +
207C PHE* 3.9 25.6 - - + -
210C LEU* 5.2 0.9 - - + -
401C LMT 4.0 44.5 - - + +
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ILE* 3.3 20.6 - - + +
307A GLN* 3.6 9.2 - - - +
309A MET* 1.3 73.3 - - - +
311A TRP* 1.3 67.0 + - - +
313A GLU* 2.9 18.0 + - - +
314A MET* 3.1 37.8 + - + +
402A LMT 4.8 29.2 - - + -
401C LMT 4.9 13.7 - - + -
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Residues in contact with TRP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A TYR* 3.3 40.8 + + + -
307A GLN 3.2 14.2 + - - +
308A TYR 4.0 0.2 - - - +
310A VAL* 1.3 76.9 - - - +
312A ARG* 1.3 63.1 + - + +
314A MET* 3.2 28.4 + - + +
315A GLN* 2.9 53.7 + - + +
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLU* 4.6 10.1 + - - -
298A ASN* 5.7 1.1 - - - -
302A TYR* 5.4 1.1 - - - -
308A TYR* 3.0 62.5 + - + +
309A MET* 3.9 5.4 - - - +
311A TRP* 1.3 80.2 - - + +
313A GLU* 1.3 57.2 + - - +
315A GLN* 3.5 27.6 + - - +
316A ASP* 2.7 80.5 + - - +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A LYS* 5.6 3.6 + - - -
309A MET 3.0 13.7 + - - +
310A VAL* 2.9 11.9 + - - +
312A ARG* 1.3 74.5 - - - +
314A MET* 1.3 64.7 + - + +
316A ASP* 3.2 12.0 + - - +
317A THR* 3.1 42.1 + - + +
401C LMT 4.7 18.6 - - + +
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Residues in contact with MET 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A VAL* 3.1 29.4 + - + +
311A TRP* 3.4 37.2 - - + +
313A GLU* 1.3 76.3 - - + +
315A GLN* 1.3 56.1 + - - +
317A THR* 2.7 36.7 + - - -
318A LEU* 3.0 18.2 + - + +
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Residues in contact with GLN 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A TYR* 4.9 1.2 + - - -
311A TRP* 2.9 43.5 + - + +
312A ARG* 3.6 32.7 - - - +
314A MET* 1.3 76.1 - - - +
316A ASP* 1.3 60.1 + - - +
318A LEU* 4.7 5.6 - - - +
319A CYS* 3.1 39.5 + - + +
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Residues in contact with ASP 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 2.7 56.6 + - - +
313A GLU* 3.6 17.6 - - - +
314A MET 3.0 0.6 - - - -
315A GLN* 1.3 78.9 + - - +
317A THR* 1.3 62.1 + - - +
319A CYS 4.5 9.2 + - - -
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Residues in contact with THR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A GLU* 3.1 30.7 - - + +
314A MET* 2.7 23.5 + - - -
316A ASP* 1.3 79.0 - - - +
318A LEU* 1.3 71.7 + - - +
319A CYS 5.3 0.2 - - - -
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A MET* 3.0 18.8 + - + +
315A GLN* 4.4 3.6 - - - +
317A THR* 1.3 92.8 + - - +
319A CYS* 1.3 73.2 + - - +
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Residues in contact with CYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A GLN* 3.1 28.2 + - + +
316A ASP* 4.8 9.4 - - - -
317A THR 5.3 0.2 - - - -
318A LEU* 1.3 94.1 - - - +
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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