Contacts of the helix formed by residues 294 - 301 (chain G) in PDB entry 2HAK
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 SER 294 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292G ARG 3.5 3.2 + - - -
293G GLY* 1.3 69.6 - - - -
295G LEU* 1.3 54.1 + - - +
296G GLU* 3.1 20.5 + - - +
297G GLN* 2.5 65.7 + - - +
298G ILE* 2.4 41.7 + - - +
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Residues in contact with LEU 295 (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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160G VAL* 4.3 16.1 - - + +
163G VAL* 5.0 12.3 - - + -
164G GLN* 3.6 39.5 - - + +
167G HIS* 5.0 14.6 - - + -
229G PRO 5.1 8.3 - - - +
230G GLU* 6.0 1.8 - - + -
232G ASP* 5.3 4.9 - - + +
233G VAL* 3.7 26.0 - - + -
236G LEU* 5.0 9.6 - - + -
293G GLY 3.7 3.2 + - - +
294G SER* 1.3 69.1 - - - +
296G GLU* 1.3 68.5 + - - +
298G ILE* 3.8 12.1 - - + +
299G MET* 2.7 41.9 + - + +
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Residues in contact with GLU 296 (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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164G GLN* 4.7 10.5 + - + +
294G SER* 3.3 14.4 + - - +
295G LEU* 1.3 98.9 + - - +
297G GLN* 1.3 61.6 - - - +
299G MET* 3.5 14.6 - - + +
300G LYS* 3.4 17.5 + - - +
315G PRO* 4.6 18.7 - - + +
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Residues in contact with GLN 297 (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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283G LYS* 5.5 5.7 + - + +
292G ARG 4.1 7.1 - - - +
293G GLY* 4.6 0.9 - - - -
294G SER* 2.5 50.7 + - - +
296G GLU* 1.3 69.6 - - - +
298G ILE* 1.3 56.2 + - + +
299G MET 2.9 1.6 - - - -
300G LYS* 2.4 33.7 + - + +
301G ASP* 2.9 10.5 + - - -
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Residues in contact with ILE 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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156G PHE* 4.3 7.9 - - + -
160G VAL* 4.5 12.8 - - + -
233G VAL* 3.8 26.2 - - + -
236G LEU* 6.0 1.1 - - + -
280G LEU* 3.9 22.2 - - + -
283G LYS* 4.6 10.5 - - + +
284G LEU* 3.6 26.9 - - + -
292G ARG 5.6 1.8 - - - +
293G GLY 5.0 0.4 - - - -
294G SER 2.4 34.6 + - - +
295G LEU* 3.8 11.2 - - + +
297G GLN* 1.3 73.2 - - + +
299G MET* 1.3 60.4 + - - +
301G ASP* 3.3 15.2 + - - +
304G MET* 3.3 30.3 - - + +
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Residues in contact with MET 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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160G VAL* 4.2 9.2 - - + +
161G SER* 5.0 4.3 - - - -
164G GLN* 3.8 27.8 - - + +
295G LEU* 2.7 39.1 + - + +
296G GLU* 3.5 10.3 - - - +
297G GLN 2.8 0.2 + - - -
298G ILE* 1.3 73.3 - - - +
300G LYS* 1.3 54.4 + - - +
304G MET* 4.5 0.8 - - - +
305G ASN* 2.8 27.4 + - - -
312G GLU* 4.3 0.7 - - - +
313G LEU* 3.1 52.1 - - + +
314G LYS* 3.1 10.5 - - - +
315G PRO* 3.1 50.3 - - + -
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Residues in contact with LYS 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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296G GLU 3.4 8.6 + - - +
297G GLN* 2.4 29.4 + - + +
299G MET* 1.3 67.5 - - - +
301G ASP* 1.3 65.2 + - - +
302G ARG* 4.7 0.3 - - - -
305G ASN* 4.0 3.2 + - - +
312G GLU* 3.6 23.0 - - - +
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Residues in contact with ASP 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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276G ASP 5.4 0.7 - - - +
279G ASN* 5.3 2.3 - - - +
280G LEU* 3.1 39.2 + - + +
283G LYS* 3.1 35.2 + - - +
297G GLN 2.9 6.4 + - - +
298G ILE* 3.3 21.8 + - - +
300G LYS* 1.3 77.5 - - - +
302G ARG* 1.3 82.1 + - - +
303G TRP* 3.1 19.8 + - - +
304G MET* 3.2 3.6 + - + +
305G ASN* 2.8 30.7 + - - +
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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