Contacts of the strand formed by residues 335 - 340 (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 335 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302P ASN 4.8 5.5 + - - +
303P LYS 3.1 9.5 + - - +
304P ALA* 4.0 18.2 - - + -
305P ALA* 2.9 25.2 + - - -
329P ALA* 5.0 2.9 - - + -
333P GLY 5.5 2.5 - - - +
334P TRP* 1.3 76.6 - - - +
336P ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 336 (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* 4.3 26.2 - - + -
287P LEU* 4.6 6.1 - - + -
305P ALA* 3.5 4.5 - - + +
307P VAL* 3.8 21.8 - - + -
325P ALA* 4.7 7.5 - - + +
328P ALA* 4.0 17.5 - - + +
329P ALA* 3.9 36.2 - - + +
332P THR* 4.2 7.0 - - + +
334P TRP* 3.7 9.5 + - + +
335P LYS* 1.3 81.2 - - - +
337P ASP* 1.3 63.7 + - - +
338P ILE* 4.0 23.4 + - + +
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Residues in contact with ASP 337 (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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298P LEU* 5.2 6.3 - - + -
305P ALA 2.9 13.2 + - - +
306P ARG* 3.4 16.9 - - + +
307P VAL 2.7 32.4 + - - -
336P ILE* 1.3 76.0 - - - +
338P ILE* 1.3 59.8 + - - +
339P LYS* 3.2 40.2 + - - +
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Residues in contact with ILE 338 (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* 4.3 11.0 - - + -
307P VAL* 3.4 12.6 - - + +
309P VAL* 3.8 27.1 - - + -
314P LEU* 4.1 18.0 - - + +
317P ALA* 3.8 32.8 - - + +
318P ILE* 4.0 14.8 - - + +
325P ALA* 3.4 33.0 - - + -
336P ILE* 4.0 12.3 + - + +
337P ASP* 1.3 74.5 + - - +
339P LYS* 1.3 84.0 + - - +
340P PRO* 4.6 1.8 - - - +
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Residues in contact with LYS 339 (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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306P ARG* 4.5 17.0 - - + +
307P VAL 2.8 6.4 + - - +
308P LEU* 3.2 25.4 - - + -
309P VAL* 2.8 29.2 + - - -
337P ASP* 3.2 35.5 + - - +
338P ILE* 1.3 92.4 + - - +
340P PRO* 1.3 71.5 - - + +
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Residues in contact with PRO 340 (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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308P LEU* 4.5 3.3 - - - +
309P VAL* 3.0 12.8 - - + +
311P PRO* 4.6 17.9 - - + -
314P LEU* 4.2 31.6 - - + -
338P ILE 4.6 0.9 - - - +
339P LYS* 1.3 99.6 - - + +
341P ILE* 1.3 68.9 + - - +
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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