Contacts of the helix formed by residues 297 - 311 (chain G) in PDB entry 1HVU
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 GLU 297 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296G THR* 1.4 76.1 - - - +
298G GLU* 1.3 67.9 + - - +
300G GLU* 4.3 10.3 - - - -
301G LEU* 3.0 29.5 + - + +
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Residues in contact with GLU 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278G GLN* 4.2 30.3 - - + +
295G LEU* 5.5 2.5 - - + -
296G THR* 2.8 8.7 + - - +
297G GLU* 1.3 83.6 - - - +
299G ALA* 1.3 63.5 + - - +
301G LEU* 4.2 0.9 - - - +
302G GLU* 3.0 22.7 + - - +
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Residues in contact with ALA 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278G GLN 5.5 0.4 + - - -
279G LEU* 5.0 16.7 - - + +
295G LEU* 3.1 39.3 - - + +
296G THR 2.7 9.9 + - - +
298G GLU* 1.3 78.6 - - - +
300G GLU* 1.3 66.4 + - - +
302G GLU* 3.2 11.8 + - - +
303G LEU* 3.5 10.7 + - - +
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Residues in contact with GLU 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295G LEU 4.3 2.2 + - - +
296G THR 3.1 11.5 + - - +
297G GLU* 4.3 8.3 - - - +
299G ALA* 1.3 80.5 - - - +
301G LEU* 1.3 62.5 + - - +
303G LEU* 3.6 11.5 + - - +
304G ALA* 3.9 8.5 + - - +
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Residues in contact with LEU 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297G GLU* 3.0 22.1 + - + +
298G GLU 4.2 0.2 - - - +
300G GLU* 1.3 75.6 - - - +
302G GLU* 1.3 67.2 + - - +
304G ALA* 3.2 17.9 + - - +
305G GLU* 3.3 12.3 + - - +
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Residues in contact with GLU 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G ILE 5.5 0.9 - - - +
276G VAL* 4.7 24.2 - - + -
278G GLN* 5.9 3.4 - - + -
279G LEU* 5.3 7.2 - - + +
298G GLU 3.0 20.7 + - - +
299G ALA* 3.2 5.6 + - - +
301G LEU* 1.3 76.0 - - - +
303G LEU* 1.3 64.8 + - - +
304G ALA 3.2 0.9 + - - -
305G GLU* 3.4 6.0 + - - +
306G ASN* 3.2 21.8 + - - +
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Residues in contact with LEU 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276G VAL* 6.0 0.6 - - - +
299G ALA 3.5 7.2 + - - +
300G GLU* 3.9 9.2 - - - +
301G LEU 3.3 0.6 - - - -
302G GLU* 1.3 76.9 - - - +
304G ALA* 1.3 56.7 + - - +
306G ASN* 3.1 9.6 - - - +
307G ARG* 2.8 28.3 + - - +
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Residues in contact with ALA 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300G GLU 3.9 5.0 + - - +
301G LEU* 3.2 14.8 + - - +
303G LEU* 1.3 74.9 - - - +
305G GLU* 1.3 62.1 + - - +
307G ARG* 2.8 25.4 + - - +
308G GLU* 2.9 13.2 + - - +
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Residues in contact with GLU 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301G LEU 3.3 8.2 + - - +
302G GLU* 3.9 8.5 - - - +
304G ALA* 1.3 77.8 - - - +
306G ASN* 1.3 63.4 + - - +
308G GLU* 3.5 9.3 + - - +
309G ILE* 3.5 16.5 + - - +
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Residues in contact with ASN 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264G LEU* 6.0 4.0 - - + -
274G ILE* 4.5 30.1 - - + +
276G VAL* 6.5 0.7 - - + -
302G GLU 3.2 10.5 + - - +
303G LEU* 3.1 14.6 - - - +
304G ALA 3.0 0.4 - - - -
305G GLU* 1.3 77.3 - - - +
307G ARG* 1.3 64.9 + - - +
309G ILE* 3.1 9.5 + - - +
310G LEU* 2.9 22.5 + - - +
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Residues in contact with ARG 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246G LEU* 5.9 9.0 - - + -
303G LEU 2.8 12.7 + - - +
304G ALA* 2.8 13.6 + - - +
306G ASN* 1.3 75.8 - - - +
308G GLU* 1.3 56.2 + - - +
310G LEU* 2.6 30.9 + - - +
311G LYS* 2.7 14.5 + - - +
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Residues in contact with GLU 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304G ALA 2.9 10.7 + - - +
305G GLU* 3.6 13.9 - - - +
307G ARG* 1.3 75.7 - - - +
309G ILE* 1.3 64.1 + - - +
311G LYS* 3.4 16.4 + - - +
312G GLU* 4.1 3.6 + - - +
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Residues in contact with ILE 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271G TYR* 5.3 13.8 - - + +
272G PRO 4.8 13.9 - - - +
273G GLY 4.9 6.3 - - - +
274G ILE* 6.1 1.6 - - + -
305G GLU 3.5 6.9 + - - +
306G ASN* 3.1 10.0 + - - +
307G ARG 3.0 0.4 - - - -
308G GLU* 1.3 81.1 - - - +
310G LEU* 1.3 64.2 + - - +
311G LYS 3.1 1.7 + - - -
312G GLU* 3.6 16.8 + - - +
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Residues in contact with LEU 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243G PRO* 3.5 20.6 - - - +
244G ILE* 3.8 29.2 + - + +
246G LEU* 5.9 4.0 - - + -
267G ALA* 6.4 2.0 - - + -
271G TYR* 5.6 6.5 - - - +
306G ASN 2.9 13.3 + - - +
307G ARG* 2.6 19.4 + - - +
309G ILE* 1.3 73.2 - - - +
311G LYS* 1.3 61.7 + - - +
312G GLU 4.4 2.4 - - - +
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Residues in contact with LYS 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243G PRO* 3.2 15.3 - - - +
307G ARG 2.7 13.2 + - - +
308G GLU* 3.5 14.8 - - - +
309G ILE 3.1 0.8 + - - -
310G LEU* 1.3 76.5 - - - +
312G GLU* 1.3 64.1 + - - +
313G PRO* 3.2 4.0 - - - +
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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