Contacts of the strand formed by residues 232 - 239 (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 ARG 232 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228P GLU* 2.9 25.4 + - - -
231P VAL* 1.3 83.1 - - + +
233P THR* 1.3 75.3 + - - +
234P LYS* 4.5 1.8 - - - -
268P GLU* 3.7 3.6 - - - +
269P LYS* 3.1 44.5 - - + +
271P ASP* 2.8 46.2 + - - +
289P PRO* 3.7 15.4 - - - +
319P GLY* 5.3 1.8 - - - -
320P LYS 5.8 0.2 - - - +
323P GLN* 3.0 42.0 + - - +
324P ASN* 3.2 28.4 + - - +
327P LEU* 3.6 25.0 - - + +
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Residues in contact with THR 233 (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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204P VAL* 4.0 9.0 - - + +
225P ILE* 3.7 22.9 - - + -
226P ALA 3.3 13.2 - - - +
227P ARG* 3.1 19.3 - - + +
232P ARG* 1.3 75.8 - - - +
234P LYS* 1.3 70.4 + - - +
265P LEU* 6.1 0.4 - - - -
268P GLU* 2.7 24.3 + - - -
269P LYS 2.8 9.9 + - - -
270P LEU* 3.2 19.7 - - + +
271P ASP 2.7 31.2 + - - -
327P LEU* 4.8 0.2 - - - -
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Residues in contact with LYS 234 (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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225P ILE* 3.3 4.3 - - - +
226P ALA* 2.8 35.9 + - + +
232P ARG* 4.6 1.8 - - + +
233P THR* 1.3 76.3 - - - +
235P VAL* 1.3 60.5 + - - +
271P ASP* 2.5 41.6 + - + +
273P LEU* 4.0 14.7 - - + +
286P ALA* 3.0 28.4 + - + +
288P ALA 3.0 7.7 + - - -
324P ASN* 2.9 42.3 + - - +
327P LEU* 3.7 27.5 - - + +
328P ALA* 4.0 9.0 - - - +
331P LEU* 3.4 10.2 - - + +
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Residues in contact with VAL 235 (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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208P MET* 3.9 32.5 - - + -
222P ILE* 3.6 23.8 - - + -
224P ALA 3.4 12.8 - - - +
225P ILE* 4.3 15.9 - - + -
234P LYS* 1.3 75.6 - - - +
236P ALA* 1.3 65.3 + - - +
237P VAL* 4.6 1.1 - - + -
270P LEU* 3.8 22.4 - - + -
271P ASP 3.0 10.1 + - - +
272P VAL* 4.0 13.6 - - + +
273P LEU* 2.8 30.1 + - - +
331P LEU* 4.2 0.7 - - - -
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Residues in contact with ALA 236 (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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222P ILE* 3.8 1.4 - - - -
223P LYS 2.9 45.3 + - - +
224P ALA* 3.0 13.7 + - + +
235P VAL* 1.3 74.1 - - - +
237P VAL* 1.3 62.5 + - - +
273P LEU* 3.2 25.8 - - + +
275P TRP* 3.6 19.5 - - + -
282P LEU* 4.5 0.4 - - + -
331P LEU* 4.1 7.6 - - + +
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Residues in contact with VAL 237 (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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208P MET* 4.1 17.3 - - + -
220P VAL* 3.8 12.3 - - + -
221P GLU 3.3 11.0 - - - +
222P ILE* 4.3 7.4 - - + -
235P VAL* 4.6 3.4 - - + -
236P ALA* 1.3 78.4 - - - +
238P ALA* 1.3 60.8 + - - +
246P PRO* 3.9 13.1 - - + +
247P ILE* 3.9 20.9 - - + -
250P CYS* 4.0 22.0 - - - -
272P VAL* 4.0 11.2 - - + -
273P LEU 2.9 16.6 + - - +
274P LYS* 3.5 6.8 - - - +
275P TRP* 2.7 28.2 + - - -
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Residues in contact with ALA 238 (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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220P VAL* 3.4 3.5 - - - -
221P GLU* 2.8 34.9 + - + +
223P LYS* 3.6 28.7 - - + -
237P VAL* 1.3 76.0 - - - +
239P SER* 1.3 64.3 + - - +
240P ASN* 5.6 2.5 - - - +
246P PRO* 4.0 7.4 - - - -
274P LYS* 5.4 3.4 - - - +
275P TRP* 4.1 13.0 - - + +
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Residues in contact with SER 239 (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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219P ILE 3.5 6.1 + - - -
220P VAL* 4.5 0.7 - - - +
238P ALA* 1.3 75.5 - - - +
240P ASN* 1.3 67.1 + - - +
241P ASP 2.8 20.2 + - - -
242P PRO* 5.0 2.1 - - - +
244P VAL* 2.7 39.5 + - - +
246P PRO* 3.6 22.9 - - - +
274P LYS* 5.7 2.0 - - - +
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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