Contacts of the helix formed by residues 331 - 340 (chain P) in PDB entry 3HX0
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 SER 331 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270P GLN* 6.0 0.9 - - - -
329P SER* 3.2 14.2 + - - -
330P GLU* 1.3 77.8 - - - +
332P VAL* 1.3 68.1 + - - +
333P PRO 3.2 2.9 - - - -
334P VAL* 2.8 16.6 + - - +
335P LEU* 2.9 36.7 + - - -
353P TYR* 3.5 30.8 + - - -
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Residues in contact with VAL 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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265P LYS 5.3 0.4 - - - +
266P ALA* 4.0 32.3 - - + +
269P VAL* 4.4 8.9 - - + +
270P GLN* 3.9 20.4 - - + +
328P ILE* 3.3 32.1 - - + -
329P SER* 3.9 4.7 - - - +
331P SER* 1.3 75.6 - - - +
333P PRO* 1.3 72.0 - - + +
335P LEU* 4.5 7.8 - - + +
336P GLU* 3.0 33.7 + - + +
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Residues in contact with PRO 333 (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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328P ILE* 5.8 0.2 - - + -
329P SER 4.2 3.1 - - - +
330P GLU* 3.5 17.5 - - - +
331P SER 3.3 5.2 - - - -
332P VAL* 1.3 99.2 - - + +
334P VAL* 1.3 63.7 + - + +
336P GLU* 3.7 12.2 - - - +
337P LEU* 3.3 18.2 + - - +
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Residues in contact with VAL 334 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330P GLU 4.6 6.3 - - - +
331P SER 2.8 6.6 + - - +
333P PRO* 1.3 71.1 - - + +
335P LEU* 1.3 66.3 + - - +
336P GLU 3.1 1.6 - - - -
337P LEU* 2.7 27.4 + - + +
338P PHE* 3.1 35.7 + - + -
353P TYR* 3.4 38.1 - - + -
358P ARG* 3.8 33.2 - - + +
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Residues in contact with LEU 335 (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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269P VAL* 4.3 26.2 - - + +
270P GLN* 4.8 17.0 - - + +
331P SER* 2.9 41.7 + - - +
332P VAL* 4.1 4.7 - - - +
334P VAL* 1.3 73.7 - - - +
336P GLU* 1.3 62.2 + - - +
338P PHE* 3.4 2.0 + - - +
339P SER* 3.0 24.1 + - - -
349P ALA* 3.5 42.7 - - + +
350P GLN* 3.7 16.2 - - + +
353P TYR* 3.7 18.4 - - + -
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Residues in contact with GLU 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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265P LYS* 4.9 17.2 - - - +
269P VAL* 3.9 20.6 - - + +
332P VAL* 3.0 23.9 + - + +
333P PRO* 3.7 10.4 - - - +
335P LEU* 1.3 72.8 - - - +
337P LEU* 1.3 59.6 + - - +
339P SER* 2.7 22.1 + - - +
340P ASN* 2.6 34.8 + - - +
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Residues in contact with LEU 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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333P PRO 3.3 10.9 + - - +
334P VAL* 2.7 19.2 + - - +
336P GLU* 1.3 75.5 + - - +
338P PHE* 1.3 70.6 + - + +
340P ASN* 3.2 14.5 + - - +
358P ARG 4.2 19.3 - - - +
359P SER* 4.2 9.6 - - - -
360P LEU* 4.1 23.3 - - + +
380P TYR* 3.0 54.6 + - + +
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Residues in contact with PHE 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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334P VAL* 3.1 35.2 + - + -
335P LEU 3.7 5.6 - - - +
337P LEU* 1.3 83.2 - - + +
339P SER* 1.3 56.7 + - - +
340P ASN 2.8 10.9 + - - -
341P ILE* 2.8 32.2 + - + +
344P ALA* 3.7 5.2 - - - +
349P ALA* 3.8 18.2 - - + -
352P TRP* 3.5 48.7 - + + -
353P TYR* 3.8 9.4 - - + -
357P PHE 4.0 16.2 - - - -
358P ARG 4.0 3.1 - - - -
359P SER 3.8 14.8 - - - -
360P LEU* 4.7 4.5 - - + -
363P ILE* 3.5 30.1 - - + -
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Residues in contact with SER 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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269P VAL* 3.4 20.8 - - - +
335P LEU 3.0 14.3 + - - -
336P GLU* 2.7 25.6 + - - +
338P PHE* 1.3 74.6 - - - +
340P ASN* 1.3 55.4 + - - +
341P ILE 3.2 0.2 - - - -
344P ALA* 3.3 13.0 - - - +
345P GLY* 4.5 18.6 - - - -
346P THR* 5.0 0.9 - - - -
349P ALA* 4.3 2.8 - - - +
809P NA 2.4 30.2 - - - -
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Residues in contact with ASN 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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336P GLU* 2.6 35.1 + - - +
337P LEU* 3.2 15.6 + - - +
338P PHE 2.8 0.4 + - - -
339P SER* 1.3 77.6 + - - +
341P ILE* 1.3 65.8 + - - +
342P TRP* 3.2 3.8 + - - -
380P TYR* 3.2 29.6 + - + +
383P PHE* 6.2 0.3 - - - +
384P LEU* 4.2 24.0 - - + +
809P NA 3.8 1.9 - - - -
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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