Contacts of the helix formed by residues 322 - 333 (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 GLY 322 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318P ILE* 3.1 30.9 - - - +
319P GLY 2.9 6.7 + - - -
321P GLY* 1.3 77.7 - - - +
323P GLN* 1.3 53.3 + - - +
324P ASN 3.2 0.3 + - - -
325P ALA* 3.3 4.1 + - - +
326P ARG* 2.7 41.6 + - - +
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Residues in contact with GLN 323 (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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228P GLU* 4.6 6.1 - - - +
231P VAL* 3.6 27.2 - - + +
232P ARG* 3.0 32.1 + - - +
269P LYS* 3.1 17.4 + - - +
318P ILE 3.6 0.6 + - - -
320P LYS* 3.3 39.9 + - - +
321P GLY 3.3 2.8 + - - -
322P GLY* 1.3 77.8 - - - +
324P ASN* 1.3 60.5 + - - +
326P ARG* 3.7 20.1 - - - +
327P LEU* 3.0 35.9 + - + +
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Residues in contact with ASN 324 (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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232P ARG* 3.2 20.7 + - - +
234P LYS* 2.9 32.4 + - - +
287P LEU* 2.9 32.5 + - - +
288P ALA 3.5 2.6 - - - +
289P PRO* 3.9 3.9 + - - -
316P LEU 3.7 7.1 + - - +
317P ALA* 2.9 26.1 + - - +
318P ILE 3.1 9.6 + - - +
319P GLY* 3.8 7.9 - - - -
323P GLN* 1.3 78.9 - - - +
325P ALA* 1.3 61.5 + - - +
327P LEU 3.5 0.3 + - - -
328P ALA* 3.0 27.9 + - - +
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Residues in contact with ALA 325 (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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287P LEU* 4.0 12.6 - - + -
317P ALA 3.5 0.6 + - - -
318P ILE* 3.1 16.8 + - + +
322P GLY* 4.0 2.9 - - - +
324P ASN* 1.3 77.1 - - - +
326P ARG* 1.3 61.4 + - - +
328P ALA* 3.7 1.2 - - - +
329P ALA* 2.9 30.7 + - - +
336P ILE* 4.7 9.8 - - + +
338P ILE* 3.4 31.0 - - + -
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Residues in contact with ARG 326 (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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228P GLU* 2.9 40.6 + - - +
320P LYS 5.1 0.2 + - - -
321P GLY 2.5 34.2 + - - -
322P GLY* 2.7 24.1 + - - +
323P GLN* 3.7 15.7 - - - +
325P ALA* 1.3 74.1 - - - +
327P LEU* 1.3 63.5 + - + +
329P ALA* 3.3 6.3 + - - +
330P LYS* 3.1 23.7 + - + +
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Residues in contact with LEU 327 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226P ALA* 3.4 32.6 - - + +
227P ARG 4.2 0.9 - - - +
228P GLU* 3.5 37.7 - - + +
231P VAL* 5.5 0.4 - - + -
232P ARG* 3.6 46.4 - - + +
233P THR 4.6 0.2 - - - +
234P LYS* 3.7 22.7 - - + -
323P GLN* 3.0 25.5 + - + +
326P ARG* 1.3 77.1 - - + +
328P ALA* 1.3 58.1 + - - +
330P LYS* 3.3 6.4 + - + -
331P LEU* 2.9 31.0 + - - +
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Residues in contact with ALA 328 (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* 4.0 7.6 - - - +
286P ALA* 3.8 23.1 - - + +
287P LEU* 3.6 25.1 - - + -
324P ASN 3.0 19.0 + - - +
325P ALA 3.7 2.9 - - - +
326P ARG 3.2 0.2 - - - -
327P LEU* 1.3 77.6 - - - +
329P ALA* 1.3 61.2 + - - +
331P LEU* 3.9 1.4 - - - +
332P THR* 2.8 32.7 + - - +
336P ILE* 4.0 8.1 - - + -
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Residues in contact with ALA 329 (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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325P ALA 2.9 17.6 + - - +
326P ARG* 3.7 5.8 - - - +
328P ALA* 1.3 76.4 - - - +
330P LYS* 1.3 59.8 + - - +
332P THR* 3.2 2.0 + - - -
333P GLY* 2.8 28.8 + - - -
334P TRP 3.3 24.3 - - - +
335P LYS* 5.0 1.8 - - + -
336P ILE* 3.9 14.8 - - + +
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Residues in contact with LYS 330 (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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201P PRO* 6.2 1.8 - - - +
225P ILE 5.2 3.1 - - - +
226P ALA* 4.1 20.9 - - + +
227P ARG 4.4 16.7 + - - +
228P GLU* 6.3 1.1 - - + +
326P ARG* 3.1 18.2 + - + +
327P LEU* 3.8 9.4 - - + +
329P ALA* 1.3 79.4 - - - +
331P LEU* 1.3 62.5 + - - +
332P THR 3.4 0.2 + - - -
333P GLY* 3.6 7.0 + - - -
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Residues in contact with LEU 331 (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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224P ALA* 3.6 29.0 - - + +
225P ILE* 3.5 26.7 - - - +
226P ALA* 3.7 8.7 - - + +
234P LYS* 3.4 37.9 - - + +
235P VAL 4.4 0.2 - - - -
236P ALA* 4.1 16.4 - - + +
273P LEU* 4.9 6.7 - - + -
282P LEU* 4.7 10.4 - - + +
286P ALA* 5.1 4.9 - - + -
327P LEU 2.9 18.6 + - - +
328P ALA* 3.9 6.1 - - - +
330P LYS* 1.3 77.2 - - - +
332P THR* 1.3 71.0 + - + +
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Residues in contact with THR 332 (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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282P LEU* 3.8 34.3 - - + +
283P ILE* 4.1 15.3 - - + -
286P ALA* 4.2 11.4 - - + -
303P LYS* 5.0 2.8 - - - -
328P ALA 2.8 19.6 + - - +
329P ALA* 3.2 4.2 + - - -
331P LEU* 1.3 83.8 - - + +
333P GLY* 1.3 58.0 + - - +
334P TRP* 2.9 44.9 + - - +
336P ILE* 4.2 2.7 - - + +
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Residues in contact with GLY 333 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303P LYS* 3.6 22.7 - - - +
329P ALA 2.8 11.0 + - - -
330P LYS 3.6 5.5 + - - -
331P LEU 3.5 2.4 - - - -
332P THR* 1.3 78.0 - - - +
334P TRP* 1.3 61.5 + - - +
335P LYS* 4.1 2.1 + - - +
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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