Contacts of the helix formed by residues 294 - 309 (chain A) in PDB entry 3H0G
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 ILE 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A PRO* 3.7 34.9 + - + -
292A ALA 3.1 0.4 - - - -
293A HIS* 1.3 77.2 - - + +
295A VAL* 1.3 62.5 - - - +
296A SER 3.2 2.7 - - - -
297A GLU* 3.2 45.7 + - - +
298A TYR* 3.8 20.3 - - + -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A VAL* 4.5 15.8 - - + +
285A CYS* 4.5 27.1 - - + +
288A GLU 5.1 6.1 - - - +
290A ALA 4.6 3.4 - - - +
291A PRO* 4.1 13.5 - - + -
292A ALA* 3.0 34.2 + - - +
294A ILE* 1.3 77.8 - - - +
296A SER* 1.3 59.8 + - - +
298A TYR* 3.4 12.5 + - + +
299A GLU* 3.3 31.4 + - - +
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA 3.7 5.5 + - - -
293A HIS* 3.0 18.9 + - - -
295A VAL* 1.3 75.4 - - - +
297A GLU* 1.3 67.7 + - - +
298A TYR 3.2 0.2 - - - -
299A GLU* 3.1 20.8 + - - +
300A GLN* 3.0 34.1 + - - +
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Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A HIS 3.8 7.7 - - - +
294A ILE* 3.2 48.8 - - - +
296A SER* 1.3 82.3 - - - +
298A TYR* 1.3 62.7 + - + +
300A GLN* 3.7 24.7 + - - +
301A LEU* 4.1 9.4 + - - +
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Residues in contact with TYR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ALA* 4.7 4.0 - - - +
282A VAL* 4.3 21.5 - - + +
294A ILE* 3.8 28.7 - - + -
295A VAL* 3.4 11.5 + - + +
296A SER 3.2 0.4 - - - -
297A GLU* 1.3 78.0 - - + +
299A GLU* 1.3 64.5 + - - +
300A GLN 3.2 1.8 - - - -
301A LEU* 3.2 38.5 + - + +
302A LEU* 3.9 2.6 + - - +
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LYS* 3.2 42.4 - - - +
282A VAL* 3.7 5.1 - - + +
295A VAL* 3.3 28.3 + - - +
296A SER* 3.1 21.7 + - - +
298A TYR* 1.3 73.4 - - - +
300A GLN* 1.3 60.3 + - - +
301A LEU 3.0 6.0 + - - -
302A LEU* 3.3 14.3 + - - +
303A GLN* 3.3 20.5 + - - +
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ARG* 3.1 44.7 + - - +
296A SER* 3.0 25.5 + - - +
297A GLU* 3.7 16.6 - - - +
298A TYR 3.2 0.4 - - - -
299A GLU* 1.3 76.0 - - - +
301A LEU* 1.3 60.9 + - + +
303A GLN* 3.2 31.1 - - - +
304A PHE* 2.8 27.4 - - + -
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ALA* 4.9 11.7 - - + -
297A GLU 4.2 8.5 - - - +
298A TYR* 3.3 36.3 - - + +
299A GLU 3.0 1.0 - - - -
300A GLN* 1.3 76.2 - - + +
302A LEU* 1.3 60.2 + - - +
303A GLN 3.1 1.6 - - - -
304A PHE* 3.1 14.1 + - + +
305A HIS* 2.9 51.8 + - + +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 6.2 1.8 - - + -
90A LYS* 3.8 32.3 - - + +
92A VAL* 4.4 23.0 - - + +
93A PHE 5.6 0.2 + - - -
275A ILE* 3.3 46.9 - - + +
278A ALA* 4.0 20.2 - - + +
279A ASN* 3.8 24.2 - - + +
298A TYR 3.9 1.9 + - - +
299A GLU 3.3 10.0 + - - +
301A LEU* 1.3 76.4 - - - +
303A GLN* 1.3 62.4 + - + +
304A PHE 3.3 0.5 + - - -
305A HIS* 4.5 2.9 - - + +
306A VAL* 3.4 28.0 + - + +
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Residues in contact with GLN 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PRO 5.7 4.9 + - - +
92A VAL* 5.9 1.1 - - - -
93A PHE* 3.7 54.0 - - + +
95A ILE* 5.2 2.6 - - - +
187A LEU* 5.6 2.9 - - - +
188A ARG* 3.6 24.4 + - - -
210A PRO* 6.1 0.2 - - - +
299A GLU* 3.3 18.8 + - - +
300A GLN* 3.2 29.7 - - - +
302A LEU* 1.3 78.4 - - + +
304A PHE* 1.3 63.2 + - + +
306A VAL* 5.0 0.6 - - - +
307A ALA* 3.6 15.9 + - - +
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Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 3.2 39.0 - - + -
188A ARG* 3.8 26.7 - - - -
300A GLN* 2.8 31.4 + - + -
301A LEU* 3.1 18.0 + - + +
303A GLN* 1.3 82.7 - - + +
305A HIS* 1.3 62.7 + - + +
306A VAL 3.5 0.2 - - - -
307A ALA* 3.0 6.5 + - + +
308A THR* 2.8 37.5 + - + +
318A PRO* 5.0 15.5 - - + -
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Residues in contact with HIS 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LYS* 4.2 19.3 + - + +
274A ASP* 4.4 21.4 + - + +
275A ILE* 3.2 34.1 - - + +
278A ALA* 5.1 9.6 - - + +
301A LEU* 2.9 47.7 + - + +
302A LEU* 4.7 3.6 - - - +
304A PHE* 1.3 75.4 - - + +
306A VAL* 1.3 57.7 + - - +
307A ALA 2.9 8.4 + - - -
308A THR* 2.7 24.7 + - - -
309A TYR* 3.0 10.2 + - - +
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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
----------------------------------------------------------
88A LEU* 6.5 1.1 - - + -
92A VAL* 5.0 15.0 - - + -
93A PHE 4.2 20.4 - - - +
94A HIS* 5.2 3.9 + - - +
95A ILE 5.9 0.2 + - - -
242A ILE* 4.6 16.2 - - + -
245A LEU* 3.8 26.2 - - + -
275A ILE* 3.1 30.9 - - + +
302A LEU* 3.4 20.1 + - + +
303A GLN 5.0 0.7 - - - +
305A HIS* 1.3 75.5 - - - +
307A ALA* 1.3 58.3 + - - +
309A TYR* 4.1 6.5 - - + -
310A MET* 3.1 24.8 - - + +
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Residues in contact with ALA 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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94A HIS* 6.4 0.4 - - - +
95A ILE* 3.3 35.7 - - + +
187A LEU* 6.0 2.0 - - + -
303A GLN 3.6 16.7 + - - +
304A PHE* 3.0 11.8 + - + +
305A HIS 2.9 1.0 - - - -
306A VAL* 1.3 78.2 - - - +
308A THR* 1.3 53.1 + - + +
309A TYR 2.9 4.0 - - - -
310A MET* 2.6 25.4 + - - +
311A ASP* 2.7 20.4 + - - -
314A ILE* 4.1 3.3 - - + +
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Residues in contact with THR 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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271A LYS* 2.6 35.0 + - - +
304A PHE* 2.8 24.3 + - + +
305A HIS* 2.7 23.5 + - - -
307A ALA* 1.3 75.0 - - + +
309A TYR* 1.3 60.0 + - - +
310A MET 3.3 0.9 + - - -
311A ASP 4.2 1.6 - - - -
312A ASN* 3.5 23.9 + - - +
318A PRO* 4.9 10.8 - - + -
320A ALA* 3.6 22.9 - - + +
328A LEU* 3.5 3.9 - - - +
330A SER* 3.4 16.6 - - - -
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Residues in contact with TYR 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 5.8 7.4 - - + -
248A PRO* 4.2 19.7 - - + +
253A ARG* 5.4 1.9 - - - -
268A LEU* 6.2 2.5 - - + -
269A THR* 5.0 8.7 - - - -
271A LYS* 5.0 6.1 - - + -
272A LEU* 3.4 56.1 - - + +
275A ILE* 4.7 4.3 - - + -
305A HIS 3.0 15.8 + - - +
306A VAL* 4.3 11.0 - - - +
307A ALA 2.9 0.4 - - - -
308A THR* 1.3 79.5 + - - +
310A MET* 1.3 70.9 + - - +
328A LEU* 4.3 12.8 - - + -
329A LYS 5.7 3.8 - - - -
330A SER* 3.7 1.5 - - - -
331A ILE* 3.3 43.8 + - + +
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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