Contacts of the helix formed by residues 301 - 313 (chain A) in PDB entry 3QTC
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 LEU 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ARG* 3.4 32.5 - - - +
300A MET* 1.3 73.5 - - - +
302A THR* 1.3 64.9 + - - +
303A PRO* 3.5 1.8 - - - -
304A ASN* 3.3 10.6 + - - +
305A LEU* 3.2 33.0 + - + +
324A GLU* 3.6 37.0 - - + +
326A GLY 4.5 1.8 - - - +
328A CYS* 3.3 24.4 - - - -
344A MET* 3.5 33.1 - - + +
346A VAL* 3.9 21.8 - - + +
811A 0A1 4.6 1.4 + - - -
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Residues in contact with THR 302 (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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276A MET* 3.7 12.6 - - + -
300A MET* 3.5 5.9 - - - +
301A LEU* 1.3 73.8 - - - +
303A PRO* 1.4 64.9 - - - +
305A LEU* 3.0 3.3 + - - -
306A TYR* 2.8 31.3 + - + +
346A VAL* 5.2 2.3 - - - +
348A TRP* 3.7 20.9 - - + -
811A 0A1 2.5 35.1 + - + +
812A EDO 3.5 40.4 - - - +
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Residues in contact with PRO 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ILE* 4.2 13.2 - - + -
272A TYR* 3.6 25.1 - - + -
273A ILE* 5.7 0.2 - - + -
276A MET* 4.0 17.7 - - + -
300A MET* 3.7 21.3 - - + +
301A LEU 3.7 2.5 - - - -
302A THR* 1.4 93.2 - - - +
304A ASN* 1.3 65.2 + - - +
306A TYR* 3.3 6.2 + - + +
307A ASN* 3.2 25.9 + - - -
411A TRP* 3.5 32.8 - - + -
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Residues in contact with ASN 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A SER* 2.8 37.7 + - - +
265A PRO* 2.8 28.3 - - - +
268A ILE* 3.7 16.4 - - - +
272A TYR* 3.4 24.4 - - - -
298A ARG* 3.9 4.6 + - - -
300A MET 6.0 0.4 - - - -
301A LEU* 3.3 10.1 + - - +
303A PRO* 1.3 79.2 - - - +
305A LEU* 1.3 60.1 + - + +
307A ASN* 3.3 10.7 + - - +
308A TYR* 3.0 30.7 + - + -
324A GLU* 4.8 0.9 - - - +
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ILE* 4.0 23.1 - - + -
301A LEU* 3.2 21.9 + - + +
302A THR 3.0 5.6 + - - +
304A ASN* 1.3 74.7 - - - +
306A TYR* 1.3 60.9 + - - +
308A TYR* 3.6 3.6 - - + +
309A LEU* 2.9 32.7 + - - +
322A ILE* 3.8 22.8 - - + +
323A PHE* 5.1 0.7 - - - -
324A GLU* 3.8 29.4 - - + +
346A VAL* 3.8 39.3 - - + +
348A TRP* 3.7 20.0 - - + -
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Residues in contact with TYR 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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276A MET* 4.0 13.2 - - - -
302A THR* 2.8 17.6 + - + -
303A PRO 3.5 8.3 - - - +
305A LEU* 1.3 77.4 - - - +
307A ASN* 1.3 60.6 + - - +
309A LEU* 3.3 5.9 + - + +
310A ARG* 3.1 26.1 + - - +
348A TRP* 3.6 28.8 - + - -
405A ILE* 3.8 7.1 - - - +
407A LEU* 3.9 4.1 - - + +
408A ASP* 2.6 42.7 + - - -
411A TRP* 3.5 52.7 - + + -
413A ILE* 3.7 21.2 - - + +
417A TRP* 5.1 0.2 - - - -
812A EDO 3.2 29.5 + - - -
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Residues in contact with ASN 307 (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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272A TYR* 3.1 38.2 + - - -
275A ARG* 5.0 3.0 + - - +
303A PRO 3.2 13.5 + - - -
304A ASN* 3.5 8.6 - - - +
306A TYR* 1.3 77.0 - - - +
308A TYR* 1.3 65.4 + - + +
310A ARG* 2.9 36.3 + - - +
311A LYS* 3.0 39.5 + - - +
411A TRP* 3.5 15.4 - - - -
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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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260A LEU* 6.0 0.4 - - + -
262A ILE* 3.6 48.7 - - + +
263A LYS 4.9 6.4 + - - -
264A SER* 4.3 12.3 - - - -
265A PRO* 6.0 1.1 - - + -
304A ASN* 3.0 23.1 + - + +
305A LEU* 3.2 8.2 + - + +
307A ASN* 1.3 78.2 - - + +
309A LEU* 1.3 56.5 + - - +
311A LYS* 4.6 10.3 - - + -
312A LEU* 2.8 59.6 + - + +
322A ILE* 4.0 14.4 - - + -
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Residues in contact with LEU 309 (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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305A LEU 2.9 19.4 + - - +
306A TYR* 3.3 9.2 + - + +
308A TYR* 1.3 72.5 - - - +
310A ARG* 1.3 62.9 + - - +
312A LEU* 4.0 3.2 - - - +
313A ASP* 3.1 26.3 + - - +
320A ILE* 3.7 28.9 - - + +
322A ILE* 3.8 21.3 - - + -
348A TRP* 3.4 50.9 - - + +
350A MET* 3.6 31.6 - - + +
413A ILE* 3.9 14.8 - - + -
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Residues in contact with ARG 310 (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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275A ARG* 5.4 2.8 - - - +
306A TYR 3.1 10.6 + - - +
307A ASN* 2.9 40.3 + - - +
308A TYR 3.3 0.2 - - - -
309A LEU* 1.3 79.7 - - - +
311A LYS* 1.3 85.7 + - - +
313A ASP* 3.5 13.7 + - - +
314A ARG* 4.0 12.9 - - - +
411A TRP* 2.9 33.6 + - - +
412A GLY* 3.9 19.7 - - - +
413A ILE* 3.6 10.2 - - + +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ASN* 3.0 29.3 + - - +
308A TYR* 3.9 10.1 - - + +
310A ARG* 1.3 102.8 - - - +
312A LEU* 1.3 66.6 + - + +
314A ARG* 3.2 25.8 + - - +
315A ALA* 4.1 2.9 + - - +
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 3.9 18.8 - - + -
262A ILE* 4.6 0.2 - - + -
308A TYR* 2.8 49.9 + - + +
309A LEU 4.3 1.1 - - - +
311A LYS* 1.3 69.2 - - + +
313A ASP* 1.3 56.5 + - - +
314A ARG 3.0 5.6 - - - -
315A ALA* 2.9 11.0 + - + +
316A LEU* 2.8 54.9 + - + +
320A ILE* 4.3 9.6 - - + -
322A ILE* 3.7 30.5 - - + -
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Residues in contact with ASP 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU 3.1 19.5 + - - +
310A ARG* 3.7 8.1 - - - +
311A LYS 3.2 0.8 - - - -
312A LEU* 1.3 76.0 - - - +
314A ARG* 1.3 60.3 + - + +
315A ALA 3.2 0.6 + - - -
316A LEU 4.2 8.4 - - - +
318A ASP* 5.7 0.7 - - - +
320A ILE* 3.9 16.1 - - - +
350A MET* 3.9 16.7 - - + +
415A LYS* 2.8 39.5 + - - -
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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