Contacts of the helix formed by residues 345 - 354 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339K SER* 5.0 6.5 - - - -
344K ALA* 1.3 74.8 - - - +
346K THR* 1.3 67.3 + - - -
347K LYS 3.2 0.3 + - - -
348K THR* 4.0 0.4 - - - -
349K ALA* 2.9 24.9 + - - +
5M A 2.8 35.3 + - - -
6M T 4.6 3.4 - - - -
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Residues in contact with THR 346 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268K SER 3.4 18.2 + - - -
269K VAL* 3.4 15.1 + - - +
270K GLN 3.2 24.7 - - - +
271K GLY* 3.3 9.8 + - - -
339K SER* 5.3 2.5 - - - -
345K GLY* 1.3 69.7 - - - +
347K LYS* 1.3 69.4 + - + +
349K ALA* 3.2 4.7 + - - +
350K GLN* 3.0 51.9 + - - +
5M A 3.8 3.7 + - - -
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Residues in contact with LYS 347 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271K GLY* 6.1 2.3 - - - -
345K GLY 3.2 0.6 - - - -
346K THR* 1.3 80.1 - - - +
348K THR* 1.3 64.6 + - - +
350K GLN* 3.0 20.9 + - - +
351K MET* 2.9 23.4 + - - +
4M T 3.3 50.8 + - - +
5M A 3.3 18.1 + - - +
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Residues in contact with THR 348 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345K GLY 3.9 4.9 - - - -
347K LYS* 1.3 72.9 - - - +
349K ALA* 1.3 60.7 + - - +
351K MET* 3.6 15.9 + - + +
352K TRP* 3.3 51.7 + - + +
373K GLN* 3.0 33.5 + - - +
4M T 3.8 5.7 + - - -
5M A 2.8 29.3 + - - -
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Residues in contact with ALA 349 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269K VAL 5.2 0.9 - - - +
335K LEU* 3.7 36.5 - - + +
338K PHE* 3.9 20.0 - - + -
339K SER* 4.6 3.6 - - - +
344K ALA* 5.6 0.6 - - + -
345K GLY 2.9 18.3 + - - +
346K THR* 3.3 8.1 - - - +
347K LYS 3.0 0.2 + - - -
348K THR* 1.3 75.5 - - - +
350K GLN* 1.3 65.9 + - - +
352K TRP* 3.2 6.9 + - - +
353K TYR* 3.1 21.7 + - - +
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Residues in contact with GLN 350 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270K GLN 3.2 12.6 + - - +
271K GLY* 4.8 0.4 - - - -
335K LEU* 3.9 22.9 - - + -
346K THR* 3.0 44.4 + - + +
347K LYS* 3.0 21.4 + - - +
349K ALA* 1.3 74.4 - - - +
351K MET* 1.3 63.3 + - - +
353K TYR* 3.3 2.6 + - - +
354K GLN* 2.9 28.1 + - - +
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Residues in contact with MET 351 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347K LYS 2.9 11.5 + - - +
348K THR* 3.6 17.9 - - + +
349K ALA 3.2 0.2 - - - -
350K GLN* 1.3 79.4 - - - +
352K TRP* 1.3 87.5 + - + +
354K GLN* 3.5 10.4 + - - +
355K GLN* 3.0 39.3 + - - +
368K SER* 4.8 13.0 - - - +
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Residues in contact with TRP 352 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338K PHE* 3.5 38.1 - + + -
341K ILE* 3.6 28.9 - - + -
344K ALA* 4.1 11.7 - - + -
348K THR* 3.3 38.6 + - + -
349K ALA 3.2 4.3 + - - +
351K MET* 1.3 92.7 - - + +
353K TYR* 1.3 60.0 + - - +
355K GLN* 2.7 35.8 + - - +
356K GLY 3.4 0.5 + - - -
357K PHE* 3.5 32.0 + + + -
363K ILE* 3.7 14.8 - - + -
367K ALA* 4.4 4.9 - - + +
368K SER 3.5 16.9 + - - +
369K LEU* 3.2 34.8 - - + -
373K GLN* 3.7 7.0 - - + -
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Residues in contact with TYR 353 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330K GLU* 3.8 19.1 + - - +
331K SER* 3.1 42.3 + - - -
334K VAL* 3.4 41.4 - - + +
335K LEU* 4.2 12.8 - - + -
338K PHE* 4.3 0.8 - - + -
349K ALA 3.1 13.0 + - - +
350K GLN* 3.3 8.0 + - - +
352K TRP* 1.3 71.5 - - - +
354K GLN* 1.3 57.1 + - - +
355K GLN 2.8 14.4 + - - -
356K GLY 2.9 12.8 + - - -
357K PHE 3.8 9.2 + - - -
358K ARG* 3.0 44.4 + - - -
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Residues in contact with GLN 354 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350K GLN 2.9 18.5 + - - +
351K MET* 3.8 8.3 - - - +
352K TRP 3.2 0.2 - - - -
353K TYR* 1.3 77.2 - - - +
355K GLN* 1.3 61.1 + - + +
356K GLY 3.5 0.9 - - - -
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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