Contacts of the helix formed by residues 278 - 287 (chain P) in PDB entry 1HH2
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 ASP 278 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276P SER* 3.1 13.2 + - - +
277P ASP* 1.3 78.1 - - - +
279P PRO* 1.3 72.1 - - - +
280P LYS* 2.7 31.7 + - - +
281P GLN* 2.9 26.9 + - + +
282P LEU* 3.0 10.4 + - - +
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Residues in contact with PRO 279 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276P SER 5.2 0.2 - - - +
277P ASP 3.4 10.0 - - - +
278P ASP* 1.3 88.0 - - - +
280P LYS* 1.3 58.4 + - + +
282P LEU* 3.7 11.8 - - + +
283P ILE* 2.9 37.8 + - + +
297P ILE* 4.7 8.1 - - + -
334P TRP* 3.5 45.3 - - + +
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Residues in contact with LYS 280 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278P ASP* 2.7 25.2 + - - +
279P PRO* 1.3 74.1 - - + +
281P GLN* 1.3 60.9 + - - +
284P ALA* 3.2 22.9 + - - +
295P VAL* 3.5 53.6 + - + +
296P GLU* 5.2 0.2 - - - +
297P ILE* 3.9 28.7 - - + +
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Residues in contact with GLN 281 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276P SER* 3.4 22.2 - - - +
278P ASP* 2.9 15.5 + - + +
280P LYS* 1.3 77.4 - - + +
282P LEU* 1.3 60.8 + - - +
284P ALA* 3.3 9.1 + - - +
285P ASN* 2.8 59.5 + - - +
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Residues in contact with LEU 282 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236P ALA* 4.5 7.9 - - + -
273P LEU* 4.6 4.3 - - + -
274P LYS 4.3 3.6 - - - +
275P TRP* 3.5 43.3 - - + +
276P SER* 3.6 24.3 - - - +
278P ASP 3.0 11.7 + - - +
279P PRO* 3.8 12.6 - - + +
281P GLN* 1.3 77.6 - - - +
283P ILE* 1.3 58.3 + - + +
285P ASN* 3.2 4.9 + - - +
286P ALA* 2.8 30.8 + - - +
331P LEU* 4.7 5.6 - - + +
332P THR* 3.8 35.0 - - + +
334P TRP* 5.6 3.4 - - + +
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Residues in contact with ILE 283 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279P PRO* 2.9 26.4 + - + +
280P LYS 4.0 2.5 - - - +
282P LEU* 1.3 76.4 - - + +
284P ALA* 1.3 62.4 + - - +
286P ALA* 3.4 7.1 + - - +
287P LEU* 3.3 30.2 + - + +
295P VAL* 4.0 13.7 - - + -
297P ILE* 5.4 0.7 - - + -
305P ALA* 4.2 13.9 - - + -
307P VAL* 3.7 29.4 - - + -
328P ALA* 5.3 0.2 - - - +
332P THR* 4.1 19.3 - - + -
334P TRP* 3.9 38.6 - - + -
336P ILE* 4.3 13.9 - - + -
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Residues in contact with ALA 284 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280P LYS 3.2 18.8 + - - +
281P GLN* 3.7 12.8 - - - +
282P LEU 3.2 0.2 - - - -
283P ILE* 1.3 75.2 - - - +
285P ASN* 1.3 66.7 + - - +
287P LEU* 3.2 12.5 + - - +
288P ALA* 3.8 6.4 + - - +
290P ALA 5.0 2.4 - - - +
292P VAL* 4.2 34.9 - - + +
295P VAL* 4.6 2.0 - - + -
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Residues in contact with ASN 285 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273P LEU* 3.7 23.4 - - + +
274P LYS* 2.7 42.0 + - - +
275P TRP 4.7 0.2 + - - -
276P SER* 4.4 8.3 - - - -
281P GLN* 2.8 45.5 + - - +
282P LEU* 3.6 4.2 - - - +
284P ALA* 1.3 73.5 - - - +
286P ALA* 1.3 60.7 + - - +
287P LEU 3.4 0.7 + - - -
288P ALA* 3.4 19.0 + - - +
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Residues in contact with ALA 286 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234P LYS* 3.0 33.9 + - + +
273P LEU* 3.7 19.7 - - + +
282P LEU 2.8 16.4 + - - +
283P ILE* 3.6 7.2 - - - +
284P ALA 3.2 0.4 - - - -
285P ASN* 1.3 78.0 - - - +
287P LEU* 1.3 57.4 + - - +
288P ALA 3.3 1.3 - - - -
328P ALA* 3.8 19.6 - - + +
331P LEU* 5.1 4.7 - - + -
332P THR* 4.2 16.2 - - + -
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Residues in contact with LEU 287 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283P ILE* 3.3 27.1 + - + +
284P ALA 3.2 7.7 + - - +
286P ALA* 1.3 75.1 - - - +
288P ALA* 1.3 56.4 + - - +
289P PRO 2.7 27.2 - - - +
290P ALA* 3.3 10.1 - - + +
292P VAL* 4.1 11.4 - - + -
307P VAL* 3.7 33.0 - - + -
317P ALA* 4.0 22.4 - - + +
324P ASN* 2.9 13.3 + - - +
325P ALA* 4.0 11.4 - - - -
328P ALA* 3.6 23.3 - - + -
336P ILE* 4.6 8.3 - - + -
338P ILE* 4.3 10.3 - - + -
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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