Contacts of the helix formed by residues 345 - 355 (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 GLY 345 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339P SER* 4.5 11.4 - - - -
344P ALA* 1.3 74.7 - - - +
346P THR* 1.3 66.0 + - - -
348P THR* 3.5 0.9 - - - -
349P ALA* 2.9 24.3 + - - +
5R A 2.9 30.7 + - - -
6R T 4.7 2.5 - - - -
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Residues in contact with THR 346 (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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268P SER 3.6 8.5 + - - -
269P VAL* 3.5 18.2 + - - +
270P GLN 3.6 0.9 - - - -
271P GLY* 3.3 38.8 + - - +
339P SER* 5.0 1.7 - - - -
345P GLY* 1.3 68.7 - - - -
347P LYS* 1.3 69.7 + - + +
349P ALA* 2.7 18.1 + - - +
350P GLN* 2.7 49.1 + - + +
5R A 3.7 5.0 + - - -
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Residues in contact with LYS 347 (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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271P GLY* 6.4 0.7 - - - -
346P THR* 1.3 82.6 - - - +
348P THR* 1.3 61.6 + - - +
350P GLN* 3.6 22.9 + - + +
351P MET* 3.1 23.6 + - - +
4R T 3.2 53.7 + - - +
5R A 3.4 16.2 + - - +
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Residues in contact with THR 348 (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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344P ALA* 4.3 3.1 - - + -
345P GLY 3.5 9.0 + - - -
346P THR 2.9 0.2 + - - -
347P LYS* 1.3 69.5 - - - +
349P ALA* 1.3 66.2 + - - +
351P MET* 3.2 11.8 + - + +
352P TRP* 3.0 54.4 + - + +
373P GLN* 3.3 30.0 + - - +
4R T 3.8 5.0 + - - -
5R A 2.6 29.9 + - - -
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Residues in contact with ALA 349 (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 5.3 1.3 - - - +
335P LEU* 3.5 37.4 - - + +
338P PHE* 3.8 22.6 - - + -
339P SER* 4.3 3.4 - - - +
344P ALA* 5.9 0.2 - - - +
345P GLY 2.9 13.5 + - - +
346P THR* 2.7 15.1 + - - +
348P THR* 1.3 69.9 - - - +
350P GLN* 1.3 66.2 + - + +
351P MET 3.2 0.3 + - - -
352P TRP* 3.2 1.4 + - - +
353P TYR* 2.9 27.4 + - - +
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Residues in contact with GLN 350 (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 5.2 0.2 - - - +
270P GLN* 4.3 10.0 + - - +
271P GLY* 4.8 1.4 - - - -
335P LEU* 3.8 22.7 - - + -
346P THR* 2.7 48.9 + - + +
347P LYS* 3.9 28.5 - - + +
349P ALA* 1.3 71.8 - - - +
351P MET* 1.3 63.4 + - - +
353P TYR* 4.1 0.2 - - - +
354P GLN* 3.0 29.3 + - - +
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Residues in contact with MET 351 (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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347P LYS 3.1 15.9 + - - +
348P THR* 3.3 15.3 - - + +
349P ALA 3.1 0.2 - - - -
350P GLN* 1.3 76.7 - - - +
352P TRP* 1.3 89.2 + - + +
354P GLN* 3.5 12.3 - - - +
355P GLN* 2.8 49.0 + - - +
368P SER* 4.1 18.4 - - - +
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Residues in contact with TRP 352 (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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338P PHE* 3.5 42.8 - + + -
341P ILE* 3.7 27.1 - - + -
344P ALA* 4.6 2.2 - - + -
348P THR* 3.0 36.8 + - + +
351P MET* 1.3 106.1 - - + +
353P TYR* 1.3 66.8 + - - +
355P GLN* 2.9 29.5 + - - +
356P GLY 3.1 4.9 + - - -
357P PHE* 3.4 17.3 + + + +
363P ILE* 3.6 22.2 - - + -
367P ALA* 4.5 4.2 - - + +
368P SER 3.7 11.5 + - - +
369P LEU* 3.2 35.4 - - + -
373P GLN* 3.9 16.2 - - + -
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Residues in contact with TYR 353 (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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330P GLU* 3.7 27.5 + - - +
331P SER* 3.5 30.3 + - - -
334P VAL* 3.4 45.8 - - + -
335P LEU* 3.7 19.3 - - + -
338P PHE* 3.8 5.3 - - + -
349P ALA 2.9 20.8 + - - +
350P GLN 4.1 1.1 - - - +
352P TRP* 1.3 71.3 - - - +
354P GLN* 1.3 61.8 + - + +
356P GLY* 2.6 17.5 + - - -
357P PHE 3.6 9.9 - - - -
358P ARG* 2.6 53.2 + - - -
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Residues in contact with GLN 354 (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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350P GLN 3.0 14.4 + - - +
351P MET* 3.5 19.6 - - - +
353P TYR* 1.3 85.6 - - + +
355P GLN* 1.3 63.5 + - - +
356P GLY 3.2 1.6 + - - -
358P ARG* 5.2 1.3 - - - +
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Residues in contact with GLN 355 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351P MET* 2.8 38.4 + - - +
352P TRP* 3.0 16.9 - - - +
353P TYR 2.8 0.2 + - - -
354P GLN* 1.3 83.9 - - - +
356P GLY* 1.3 57.1 + - - +
357P PHE* 2.9 43.0 + - + -
367P ALA* 5.3 0.2 - - - -
368P SER* 5.0 5.9 + - - -
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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