Contacts of the helix formed by residues 295 - 304 (chain B) in PDB entry 2HOD
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 GLY 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B TYR 3.8 2.5 - - - -
270B LYS 3.1 6.5 - - - -
271B GLN 2.9 33.0 + - - -
272B GLY* 3.5 2.4 - - - -
293B TRP 2.5 11.1 + - - -
294B LEU* 1.3 81.4 - - - +
296B ASN* 1.3 67.0 + - - -
297B ASP 3.5 0.2 - - - -
298B LYS* 3.3 9.5 + - - +
299B ILE* 3.0 16.3 + - - +
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Residues in contact with ASN 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B TRP* 4.6 1.4 - - - -
269B TYR* 2.9 26.1 + - - +
270B LYS* 2.8 9.3 + - - -
293B TRP* 2.6 43.2 - - - +
295B GLY* 1.3 67.9 - - - -
297B ASP* 1.3 53.6 + - - +
299B ILE* 2.5 32.0 + - - +
300B SER* 2.7 17.0 + - - -
331B VAL* 5.1 1.9 - - + +
338B TYR* 3.3 37.3 - - + +
375B PHE* 3.6 29.2 - - - -
403B TRP* 5.7 3.2 - - - -
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LYS* 2.9 35.3 + - - +
271B GLN* 4.5 4.4 - - - +
296B ASN* 1.3 72.8 - - - +
298B LYS* 1.3 64.5 + - + +
300B SER* 3.4 3.1 + - - +
301B GLN* 3.2 23.9 + - - +
333B ASN* 5.7 0.9 - - - +
334B GLU* 4.2 11.3 + - - +
338B TYR* 2.7 34.9 + - - -
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B TYR* 2.8 69.2 + - + +
237B ARG 4.6 4.0 + - - -
270B LYS 5.2 0.2 - - - +
271B GLN 4.2 17.1 + - - +
294B LEU* 4.2 17.7 - - + +
295B GLY* 3.3 15.0 + - - +
296B ASN 3.1 0.4 - - - -
297B ASP* 1.3 78.9 - - + +
299B ILE* 1.3 57.3 + - - +
301B GLN* 3.4 8.5 + - - -
302B LEU* 3.1 32.5 + - - +
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Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ILE* 3.1 40.2 - - + -
293B TRP* 3.9 24.2 - - + -
294B LEU* 3.2 15.5 - - + +
295B GLY 3.0 9.6 - - - +
296B ASN* 2.5 23.8 + - - +
298B LYS* 1.3 68.3 - - + +
300B SER* 1.3 57.0 + - - +
301B GLN 2.8 14.2 + - - -
302B LEU* 2.8 19.9 + - + +
303B THR* 2.9 18.3 + - + -
329B PHE* 4.5 8.3 - - + -
331B VAL* 3.6 28.0 - - + -
403B TRP* 5.8 1.8 - - + -
454B ILE* 6.3 0.7 - - + -
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Residues in contact with SER 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ASN 2.7 9.4 + - - -
297B ASP* 4.0 5.2 - - - -
299B ILE* 1.3 73.9 - - - +
301B GLN* 1.3 49.6 + - - +
303B THR* 3.1 6.3 + - - -
304B ARG* 2.6 35.2 + - - +
331B VAL* 2.5 23.2 + - - +
332B GLN 2.5 30.6 + - - -
333B ASN* 2.9 12.8 + - - +
338B TYR* 3.7 20.9 - - - -
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Residues in contact with GLN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PRO* 2.9 31.9 - - - +
230B ASP* 3.8 12.5 + - + +
233B VAL* 5.1 5.3 - - + +
236B TYR* 4.3 1.6 + - - -
297B ASP 3.2 16.7 + - - +
298B LYS* 3.4 6.1 + - - +
299B ILE 2.8 1.2 + - - -
300B SER* 1.3 78.2 - - - +
302B LEU* 1.3 112.2 + - - +
303B THR 3.2 0.2 - - - -
304B ARG* 2.9 24.8 + - + +
305B MET* 3.6 12.1 + - - +
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B GLU* 5.0 11.7 - - + -
227B ILE* 4.8 2.5 - - + -
229B PRO* 4.1 8.5 - - + -
236B TYR* 3.0 23.3 - - + +
250B THR* 4.3 23.6 - - + -
252B ILE* 5.0 4.9 - - + -
294B LEU* 4.5 8.1 - - + -
298B LYS 3.1 13.7 + - - +
299B ILE* 2.8 11.9 + - + +
301B GLN* 1.3 95.4 - - - +
303B THR* 1.3 62.3 + - + +
305B MET* 3.1 35.9 + - - +
308B THR* 3.3 17.2 - - + +
454B ILE* 4.7 15.3 - - + -
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Residues in contact with THR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ILE* 2.9 14.8 + - + +
300B SER 3.1 13.9 + - - -
302B LEU* 1.3 77.2 - - + +
304B ARG* 1.3 57.9 + - - +
305B MET 2.8 9.9 + - - -
306B GLY 3.6 10.2 - - - +
308B THR* 2.4 30.5 + - + +
329B PHE* 3.8 28.5 - - + +
330B THR* 3.6 22.0 - - - +
331B VAL* 3.2 37.7 + - + +
454B ILE* 5.9 0.4 - - + -
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B SER* 2.6 26.6 + - - +
301B GLN* 2.9 16.7 + - + +
303B THR* 1.3 82.0 + - - +
305B MET* 1.3 55.8 + - - +
306B GLY 3.2 7.9 + - - -
330B THR* 6.1 3.3 - - - -
331B VAL 4.4 0.8 + - - -
332B GLN* 2.6 37.9 + - - +
333B ASN* 2.5 61.4 - - - +
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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