Contacts of the helix formed by residues 273 - 283 (chain A) in PDB entry 1H1V
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 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A LEU* 5.5 0.4 - - - -
261A LEU 3.4 12.8 - - - -
262A PHE 3.5 17.9 + - - -
264A PRO* 3.8 2.7 - - - +
272A ALA* 1.3 76.3 - - - +
274A ILE* 1.3 66.7 + - - -
275A HIS* 3.1 11.9 - - - -
276A GLU* 3.0 7.0 + - - +
277A THR* 3.0 25.5 + - - +
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Residues in contact with ILE 274 (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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153A LEU* 4.4 19.3 - - + -
160A THR* 4.1 15.0 - - + -
162A ASN* 3.9 1.0 + - - -
178A LEU* 3.9 22.7 - - + -
261A LEU* 3.3 39.6 + - + +
262A PHE* 3.9 33.4 - - + -
273A GLY* 1.3 71.2 - - - -
275A HIS* 1.3 52.8 + - - +
277A THR* 3.1 16.0 + - - +
278A THR* 2.4 30.5 + - - -
309A ILE* 4.3 12.1 - - + -
313A MET* 3.5 12.9 - - - +
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Residues in contact with HIS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PHE* 3.4 42.4 - + + -
273A GLY* 3.6 13.6 - - - -
274A ILE* 1.3 80.3 - - - +
276A GLU* 1.3 87.0 + - + +
278A THR* 3.5 2.6 + - - -
279A TYR* 3.2 22.0 + - - +
312A ARG* 5.8 0.2 - - - -
313A MET* 3.9 17.7 - - - -
316A GLU* 3.5 48.8 + - + -
317A ILE* 4.1 9.0 - - + +
320A LEU* 3.7 13.3 - - + +
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Residues in contact with GLU 276 (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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272A ALA* 3.9 20.6 - - + +
273A GLY 3.0 9.7 + - - +
275A HIS* 1.3 105.3 + - + +
277A THR* 1.3 54.8 + - - +
279A TYR* 3.1 4.1 + - - +
280A ASN* 2.6 52.6 + - - +
320A LEU* 4.3 18.0 - - + +
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Residues in contact with THR 277 (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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162A ASN* 2.6 25.1 + - - -
176A MET* 3.7 19.0 - - + +
178A LEU* 5.3 11.8 - - + +
271A SER* 4.7 6.3 - - - +
272A ALA* 4.5 17.5 - - + +
273A GLY 3.0 15.2 + - - +
274A ILE* 3.1 17.4 + - - +
276A GLU* 1.3 75.7 - - - +
278A THR* 1.3 56.2 + - - +
280A ASN* 3.6 10.6 - - - +
281A SER* 2.8 30.8 + - - -
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Residues in contact with THR 278 (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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151A ILE* 4.0 14.6 - - + -
153A LEU* 6.5 0.4 - - + -
162A ASN* 2.8 22.1 + - - +
274A ILE 2.4 25.7 + - - -
275A HIS 3.6 6.3 - - - -
276A GLU 3.1 0.2 - - - -
277A THR* 1.3 76.7 + - - +
279A TYR* 1.3 59.3 + - - +
281A SER* 3.3 4.0 + - - -
282A ILE* 2.9 42.4 + - + +
297A ASN* 4.0 13.7 - - - +
313A MET* 3.1 13.2 - - + +
317A ILE* 3.6 20.9 - - + -
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Residues in contact with TYR 279 (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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275A HIS 3.2 10.6 + - - +
276A GLU* 3.1 8.2 + - - +
278A THR* 1.3 76.3 - - - +
280A ASN* 1.3 84.4 + - - +
281A SER 2.9 1.2 + - - -
282A ILE* 3.0 9.8 + - - +
283A MET* 3.0 55.3 + - + +
294A TYR* 3.8 22.9 - + - -
317A ILE* 5.2 5.3 - - + +
320A LEU* 3.6 53.9 + - + -
321A ALA* 4.5 1.3 - - - -
322A PRO* 5.4 1.6 - - + -
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Residues in contact with ASN 280 (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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176A MET* 4.7 14.0 - - + +
272A ALA* 5.3 3.6 - - - +
276A GLU* 2.6 37.9 + - - +
277A THR* 3.6 11.2 - - - +
279A TYR* 1.3 92.3 - - - +
281A SER* 1.3 59.9 + - - +
283A MET* 3.3 13.0 + - - +
284A LYS* 3.3 17.8 + - - +
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Residues in contact with SER 281 (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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151A ILE* 3.6 7.2 - - - +
162A ASN* 4.1 3.7 + - - -
164A PRO* 2.9 24.3 - - - +
174A ALA* 2.6 27.0 + - - +
176A MET* 3.8 13.7 - - - -
277A THR 2.8 18.4 + - - -
278A THR 3.4 5.4 - - - -
280A ASN* 1.3 71.7 - - - +
282A ILE* 1.3 66.8 + - - +
283A MET 3.0 2.0 - - - -
284A LYS* 2.9 18.7 + - - +
285A CYS* 3.5 10.4 - - - -
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Residues in contact with ILE 282 (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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151A ILE* 3.9 28.7 - - + -
278A THR* 2.9 30.0 + - + +
279A TYR* 3.6 6.5 - - - +
281A SER* 1.3 76.8 - - - +
283A MET* 1.3 60.7 + - - +
284A LYS 3.2 1.0 + - - -
285A CYS* 3.2 17.4 + - - +
290A ARG* 2.9 42.5 - - + +
293A LEU* 4.3 14.8 - - + -
294A TYR* 3.6 53.6 - - + +
297A ASN* 4.8 2.2 - - - +
317A ILE* 5.3 1.6 - - + -
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Residues in contact with MET 283 (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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279A TYR* 3.0 49.8 + - + +
280A ASN* 3.5 12.8 - - - +
281A SER 3.0 0.4 - - - -
282A ILE* 1.3 75.5 - - - +
284A LYS* 1.3 59.6 + - - +
285A CYS 3.3 0.4 - - - -
290A ARG* 3.1 61.5 + - - +
294A TYR* 3.8 21.8 - - + +
322A PRO* 5.4 8.1 - - + -
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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