Contacts of the strand formed by residues 269 - 274 (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 LYS 269 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231P VAL* 3.0 18.7 + - + +
232P ARG* 3.1 43.4 - - + +
233P THR* 2.8 24.4 + - - -
262P LEU* 4.7 3.6 - - - -
265P LEU* 4.9 1.2 - - - +
267P GLY 4.7 5.6 - - - +
268P GLU* 1.3 80.8 - - - +
270P LEU* 1.3 62.4 + - - +
271P ASP* 5.0 2.2 - - - +
320P LYS* 6.1 1.4 - - - +
323P GLN* 3.1 24.4 + - - +
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Residues in contact with LEU 270 (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* 4.3 11.9 - - + -
208P MET* 5.0 7.9 - - + -
233P THR* 3.2 28.0 - - + +
235P VAL* 3.8 23.6 - - + -
258P ILE* 4.3 21.2 - - + +
261P ILE* 3.6 33.7 - - + -
262P LEU* 3.9 17.3 - - + +
265P LEU* 4.7 7.2 - - + -
268P GLU 4.0 0.4 + - - -
269P LYS* 1.3 78.2 - - - +
271P ASP* 1.3 62.1 + - - +
272P VAL* 3.7 19.6 + - + -
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Residues in contact with ASP 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232P ARG* 2.8 36.0 + - - -
233P THR 2.7 8.7 + - - +
234P LYS* 2.5 42.8 + - + +
235P VAL* 3.0 26.7 + - - +
269P LYS* 5.0 2.6 - - - +
270P LEU* 1.3 74.3 + - - +
272P VAL* 1.3 62.2 + - - +
273P LEU* 3.7 7.8 + - + +
288P ALA* 3.7 8.9 - - + +
289P PRO* 5.2 1.4 - - - +
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Residues in contact with VAL 272 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208P MET* 5.1 2.7 - - + -
235P VAL* 3.6 16.4 - - + -
237P VAL* 4.0 20.2 - - + -
247P ILE* 3.9 19.8 - - + +
250P CYS* 3.9 31.4 - - + -
251P ILE* 4.7 10.1 - - + -
258P ILE* 4.4 16.6 - - + +
270P LEU* 3.7 25.6 + - + -
271P ASP* 1.3 72.4 - - - +
273P LEU* 1.3 60.0 + - - +
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Residues in contact with LEU 273 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234P LYS* 4.0 28.9 - - + +
235P VAL 2.8 19.7 + - - +
236P ALA* 3.2 17.5 - - + -
237P VAL* 2.9 27.0 + - - +
247P ILE* 3.7 6.1 - - - -
271P ASP* 4.1 9.4 - - + +
272P VAL* 1.3 75.6 - - - +
274P LYS* 1.3 64.7 + - - +
282P LEU* 4.5 7.2 - - + +
285P ASN* 3.7 22.2 - - + +
286P ALA* 3.7 39.9 - - + +
288P ALA* 5.9 2.7 - - + +
331P LEU* 4.9 4.9 - - + -
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Residues in contact with LYS 274 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237P VAL 3.5 9.9 - - - +
238P ALA* 5.4 1.3 - - - +
239P SER* 5.7 2.9 - - - +
245P ASP* 6.1 0.2 - - - +
246P PRO* 4.4 25.1 - - + +
247P ILE* 3.7 17.6 - - + +
273P LEU* 1.3 79.5 - - - +
275P TRP* 1.3 73.8 + - - +
276P SER 3.7 0.5 + - - -
282P LEU* 4.3 1.0 - - - +
285P ASN* 2.7 40.9 + - - +
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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