Contacts of the helix formed by residues 301 - 314 (chain A) in PDB entry 1QHP
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 MET 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A VAL* 3.7 18.6 - - + -
294A PHE* 3.8 28.3 - - + -
300A THR* 1.4 75.4 - - - +
302A TYR* 1.3 61.2 + - - +
304A LEU* 3.2 15.4 + - + +
305A ASN 2.9 20.4 + - - -
415A ILE* 3.3 13.5 - - + +
416A ASN 3.2 16.2 - - - +
417A ASN 3.0 17.9 + - - +
418A ASP 3.5 28.0 - - - +
419A VAL 3.7 11.2 - - - +
420A TYR* 3.7 17.5 - - + -
435A ILE* 4.0 19.3 - - + +
437A ARG* 4.2 7.4 - - + -
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Residues in contact with TYR 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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300A THR* 3.1 9.2 + - - +
301A MET* 1.3 77.8 - - - +
303A ASP* 1.3 57.5 + - - +
305A ASN* 3.5 2.9 + - - +
306A ASN* 2.9 43.4 + - - +
415A ILE* 3.4 45.3 + - + -
416A ASN* 3.5 23.2 - - - +
417A ASN* 3.5 26.9 - - - -
1E GLC 4.6 2.6 + - - -
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Residues in contact with ASP 303 (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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289A VAL* 3.7 6.3 - - + +
299A GLN* 3.3 41.3 + - + +
300A THR* 2.8 36.8 + - - +
302A TYR* 1.3 74.6 - - - +
304A LEU* 1.3 60.4 + - - +
306A ASN* 3.3 12.6 + - - +
307A MET* 2.9 29.5 + - - +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 4.1 7.9 - - + -
289A VAL* 3.7 19.2 - - + +
290A ILE* 4.1 17.9 - - + +
293A VAL* 4.1 7.6 - - + -
294A PHE* 3.7 24.9 - - + -
300A THR 3.1 11.2 + - - +
301A MET* 3.2 27.1 + - - +
303A ASP* 1.3 77.4 - - - +
305A ASN* 1.3 62.1 + - - +
307A MET* 3.2 4.5 + - - +
308A VAL* 3.0 26.3 + - - +
349A PHE* 3.7 46.0 - - + -
420A TYR* 4.0 7.0 - - + -
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Residues in contact with ASN 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A MET 2.9 15.8 + - - +
302A TYR* 3.8 3.0 - - - +
304A LEU* 1.3 75.0 - - - +
306A ASN* 1.3 68.6 + - - +
308A VAL* 3.2 3.2 + - - +
309A ASN* 3.0 42.4 + - - +
412A GLN* 3.4 28.7 + - - +
415A ILE* 3.7 15.7 - - + +
420A TYR* 2.6 39.9 + - + +
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Residues in contact with ASN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TYR* 2.9 34.3 + - - +
303A ASP* 3.6 13.3 + - - +
304A LEU 3.3 0.2 - - - -
305A ASN* 1.3 81.6 + - - +
307A MET* 1.3 59.4 + - - +
309A ASN* 3.3 10.4 + - - +
310A GLN* 2.8 31.8 + - - +
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Residues in contact with MET 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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261A ASP* 6.1 0.2 - - + -
262A PRO* 3.8 36.6 - - + -
285A ASP* 3.6 20.4 - - - +
286A LEU* 3.9 20.2 - - + +
289A VAL* 3.9 24.2 - - + -
303A ASP 2.9 17.6 + - - +
304A LEU 3.2 4.2 + - - +
306A ASN* 1.3 74.8 - - - +
308A VAL* 1.3 61.3 + - - +
310A GLN* 3.9 16.4 - - - +
311A THR* 2.8 39.9 + - + -
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Residues in contact with VAL 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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286A LEU* 4.1 10.7 - - + +
304A LEU 3.0 18.2 + - - +
305A ASN* 3.6 7.6 - - - +
307A MET* 1.3 74.6 - - - +
309A ASN* 1.3 64.0 + - - +
311A THR* 3.1 6.6 + - - -
312A GLY* 3.0 26.2 + - - -
349A PHE* 4.0 26.0 - - + -
353A SER* 5.6 1.6 - - - +
354A ARG* 4.6 18.1 + - - +
410A THR* 4.0 33.0 - - + +
420A TYR* 4.1 13.0 - - - +
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Residues in contact with ASN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASN* 3.0 40.2 + - - +
306A ASN* 3.6 11.8 + - - +
308A VAL* 1.3 80.6 - - - +
310A GLN* 1.3 62.4 + - - +
312A GLY* 3.3 2.1 + - - -
313A ASN* 3.0 34.7 + - - +
410A THR 5.2 5.7 - - - +
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Residues in contact with GLN 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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262A PRO* 3.6 31.9 - - + +
263A GLY 5.3 1.2 - - - +
306A ASN* 2.8 21.0 + - - +
307A MET* 3.9 17.8 - - - +
308A VAL 3.4 0.2 - - - -
309A ASN* 1.3 73.6 - - - +
311A THR* 1.3 62.6 + - - +
313A ASN* 3.2 9.4 + - - +
314A GLU* 3.1 47.9 + - + +
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Residues in contact with THR 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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262A PRO* 5.5 0.9 - - + -
283A ASP* 4.3 3.8 - - - +
285A ASP* 3.7 36.6 - - + +
286A LEU 4.8 0.2 - - - +
307A MET* 2.8 34.5 + - + +
308A VAL 3.1 5.5 + - - -
310A GLN* 1.3 73.6 - - - +
312A GLY* 1.3 64.9 + - - +
314A GLU* 3.1 2.4 + - - +
315A TYR* 3.0 45.6 + - + +
318A LYS* 4.5 2.4 - - - +
321A LEU* 4.5 0.9 - - - -
354A ARG* 2.8 31.5 + - - +
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Residues in contact with GLY 312 (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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308A VAL 3.0 19.0 + - - -
309A ASN* 3.7 3.1 - - - -
310A GLN 3.2 0.4 - - - -
311A THR* 1.3 78.3 + - - +
313A ASN* 1.3 61.6 + - - +
315A TYR 4.0 3.6 - - - +
318A LYS* 3.6 41.8 + - - +
354A ARG* 5.8 1.1 - - - -
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Residues in contact with ASN 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ASN* 3.0 26.6 + - - +
310A GLN* 3.2 7.3 + - - +
312A GLY* 1.3 79.2 - - - +
314A GLU* 1.3 64.1 + - + +
315A TYR 5.2 0.2 - - - -
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Residues in contact with GLU 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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262A PRO* 4.6 1.2 - - - +
267A HIS* 2.7 40.6 + - - -
271A VAL* 3.5 19.9 - - + +
275A ASN* 3.0 22.3 + - - -
285A ASP* 4.4 0.5 - - - +
310A GLN* 3.3 39.0 + - + +
311A THR* 3.1 3.7 + - - +
313A ASN* 1.3 83.1 - - + +
315A TYR* 1.3 74.7 + - + +
316A LYS 3.6 0.3 + - - -
618A GLY* 5.5 0.5 - - - -
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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