Contacts of the helix formed by residues 305 - 316 (chain A) in PDB entry 1HT6
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 LYS 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A VAL* 3.2 40.2 - - + +
259A GLU* 2.9 31.2 + - - +
260A GLY 5.4 0.4 - - - +
301A PHE* 3.3 13.2 - - + -
302A PRO* 3.0 7.3 + - + +
304A ASP* 1.3 115.3 + - - +
306A VAL* 1.3 65.6 + - - +
307A MET 3.2 3.1 - - - +
308A GLN* 2.9 42.1 + - - +
309A GLY 3.3 1.2 + - - -
397A ASN 6.1 0.2 - - - -
398A ASP* 5.6 3.6 - - - -
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL* 4.3 2.3 - - + +
288A ASP* 5.3 0.4 - - - +
301A PHE* 3.8 23.6 - - + +
302A PRO 3.6 13.2 + - - +
303A SER* 3.9 2.6 + - - +
304A ASP 3.7 1.2 - - - -
305A LYS* 1.3 77.4 - - - +
307A MET* 1.3 58.2 + - - +
309A GLY* 2.9 17.2 + - - -
310A TYR* 3.1 36.6 + - + -
326A HIS* 3.9 20.2 - - + +
330A TRP* 3.7 26.9 - - + -
332A PHE* 3.6 24.8 - - + -
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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
----------------------------------------------------------
305A LYS* 3.2 1.2 - - - +
306A VAL* 1.3 77.1 - - - +
308A GLN* 1.3 57.3 + - - +
310A TYR* 3.3 10.0 + - + +
311A ALA* 2.8 28.9 + - - +
332A PHE* 3.5 54.7 - - + -
335A GLN* 3.7 24.2 - - + +
336A ILE* 4.0 10.3 - - + -
339A LEU* 3.7 31.2 - - + -
397A ASN* 5.0 6.7 - - + +
399A TYR* 3.7 32.2 - - + +
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Residues in contact with GLN 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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258A VAL* 4.4 19.7 - - + +
262A LEU* 4.8 2.4 - - - +
301A PHE* 5.0 0.2 - - - -
304A ASP 4.9 1.2 + - - -
305A LYS* 2.9 46.5 + - - +
307A MET* 1.3 74.3 - - - +
309A GLY* 1.3 66.0 + - - +
311A ALA* 3.3 1.1 + - - -
312A TYR* 3.0 24.6 + - - +
376A ILE* 3.7 23.8 - - + +
377A GLY* 3.2 22.4 + - - -
397A ASN 3.9 10.2 + - - +
398A ASP* 3.3 45.7 + - - +
399A TYR* 4.6 1.1 - - + -
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Residues in contact with GLY 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 4.0 11.7 - - - -
287A VAL* 3.7 11.0 - - - -
301A PHE* 3.7 22.5 - - - -
305A LYS 3.3 4.8 + - - -
306A VAL 2.9 8.8 + - - -
308A GLN* 1.3 79.6 - - - +
310A TYR* 1.3 56.7 + - - +
312A TYR* 3.4 3.1 + - - +
313A ILE* 2.9 32.7 + - - +
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Residues in contact with TYR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL* 3.7 21.4 + - + +
306A VAL* 3.1 33.8 + - + -
307A MET* 3.3 21.1 + - + +
308A GLN 3.3 0.2 - - - -
309A GLY* 1.3 70.7 - - - +
311A ALA* 1.3 67.0 + - - +
312A TYR 3.1 1.6 - - - -
313A ILE* 4.1 10.3 - - + -
314A LEU* 2.9 57.2 + - + +
321A CYS 4.4 1.2 + - - -
322A ILE* 3.9 22.9 - - + -
323A PHE* 3.1 22.0 + - - +
326A HIS* 2.6 45.3 + - + +
336A ILE* 4.0 16.6 - - + -
339A LEU* 4.1 1.7 - - - +
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Residues in contact with ALA 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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307A MET 2.8 18.9 + - - +
308A GLN 3.3 5.1 + - - +
310A TYR* 1.3 76.2 - - - +
312A TYR* 1.3 51.8 + - - +
315A THR* 2.8 37.4 + - - +
339A LEU* 4.0 14.0 - - + +
374A VAL* 3.7 13.3 - - + +
376A ILE* 3.8 7.2 - - + -
399A TYR* 3.7 36.1 - - + -
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Residues in contact with TYR 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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250A THR* 3.8 19.7 + - + +
254A LEU* 3.8 22.0 - - + -
265A LEU* 4.0 32.0 + - + +
272A ALA* 4.1 11.8 - - - +
273A PRO* 4.4 5.5 - - - +
276A MET* 3.6 30.1 - - + +
308A GLN 3.0 17.1 + - - +
309A GLY 3.5 4.0 - - - +
311A ALA* 1.3 74.0 - - - +
313A ILE* 1.3 74.4 + - + +
315A THR* 3.2 6.8 + - - -
316A HIS* 3.0 55.8 + + - +
364A TYR* 3.7 26.0 + + - -
374A VAL* 5.3 1.1 - - - -
376A ILE* 4.4 10.2 - - + +
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Residues in contact with ILE 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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250A THR* 5.0 2.5 - - + -
254A LEU* 4.5 8.3 - - + -
276A MET* 5.3 1.1 - - - -
285A THR* 3.5 32.8 + - + +
286A PHE* 3.7 31.2 - - - +
287A VAL* 3.9 13.0 - - + -
309A GLY 2.9 25.9 + - - +
310A TYR* 4.1 16.4 - - + -
312A TYR* 1.3 90.5 - - + +
314A LEU* 1.3 66.5 + - + +
315A THR 3.4 0.7 + - - -
316A HIS* 3.5 13.7 + - - +
317A PRO 4.9 1.0 - - - +
320A PRO* 3.6 20.2 - - + +
321A CYS 3.9 13.0 - - - +
343A ARG* 3.5 7.6 + - - -
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Residues in contact with LEU 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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3A VAL* 4.8 1.3 - - + -
310A TYR* 2.9 43.8 + - + +
311A ALA 5.0 0.2 - - - +
313A ILE* 1.3 75.1 - - + +
315A THR* 1.3 59.1 + - - +
320A PRO* 3.7 26.5 - - + -
322A ILE* 4.0 17.3 - - + -
336A ILE* 3.9 27.1 - - + +
339A LEU* 3.7 36.1 - - + +
340A VAL* 4.0 17.7 - - + +
343A ARG* 2.9 36.6 + - - +
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Residues in contact with THR 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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311A ALA 2.8 24.9 + - - +
312A TYR 3.3 0.2 + - - -
313A ILE 3.2 0.2 - - - -
314A LEU* 1.3 79.7 - - - +
316A HIS* 1.3 77.1 + - - +
339A LEU* 4.5 18.4 - - + +
342A ILE* 5.2 5.8 - - + -
343A ARG* 3.8 3.1 - - - +
348A ILE* 3.8 11.9 - - - +
368A ILE* 3.3 35.7 - - - +
372A VAL* 4.3 15.7 - - + -
374A VAL* 3.5 21.5 - - + +
401A VAL* 4.7 4.3 - - + -
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Residues in contact with HIS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A MET* 3.8 15.0 - - + -
312A TYR* 3.0 35.2 + + - +
313A ILE 3.5 5.3 + - - +
315A THR* 1.3 99.5 + - - +
317A PRO* 1.3 76.9 - - + +
318A GLY 3.7 0.3 - - - +
343A ARG* 2.8 24.1 + - - -
348A ILE* 4.7 2.2 - - - -
354A LEU* 3.6 25.1 - - + +
364A TYR* 2.6 38.7 + + - -
366A ALA* 3.9 6.1 - - + -
368A ILE* 4.1 5.9 - - + +
374A VAL* 3.6 26.5 - - + -
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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