Contacts of the helix formed by residues 309 - 317 (chain H) in PDB entry 5LXY
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 PHE 309 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G LEU* 3.4 32.1 - - + -
32G GLN* 4.1 23.8 - - + +
69G LEU* 4.3 10.8 - - + -
70G LEU* 3.5 25.6 - - + -
73G ILE* 4.3 16.4 - - + -
291H ILE* 4.7 7.6 - - + -
299H LEU* 3.8 29.6 - - + -
307H PRO 4.0 0.4 + - - -
308H PRO* 1.3 82.8 - - + +
310H ILE* 1.3 56.4 + - - +
311H TYR 3.3 2.8 - - - +
312H ARG* 3.4 4.2 + - - +
313H MET* 2.8 46.9 + - - +
401H BR 3.9 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 310 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H PRO* 3.6 41.3 - - + +
289H GLY* 3.7 8.5 - - - +
307H PRO* 4.1 27.1 + - + +
308H PRO 2.9 13.7 + - - +
309H PHE* 1.3 78.3 - - - +
311H TYR* 1.3 57.2 + - - +
313H MET* 3.9 10.7 - - + +
314H ARG* 2.8 60.5 + - + +
306L LEU* 4.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 311 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H PRO 5.2 1.6 + - - -
309H PHE* 3.3 1.0 - - - +
310H ILE* 1.3 81.6 - - - +
312H ARG* 1.3 62.3 + - + +
314H ARG* 3.6 21.1 + - - +
315H GLN* 3.1 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 312 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ASN* 3.4 23.7 + - - +
69G LEU* 3.6 32.3 - - + +
309H PHE* 3.4 4.2 + - - +
311H TYR* 1.3 78.5 - - - +
313H MET* 1.3 65.9 + - - +
315H GLN* 2.9 43.5 + - - +
316H LEU* 3.1 54.4 + - + +
401H BR 4.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 313 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G GLN* 4.3 20.0 - - - +
65G TYR* 3.5 16.2 - - - +
69G LEU* 3.8 23.6 - - + -
286H PHE* 3.7 24.7 - - + -
288H PRO* 3.9 4.0 - - + -
309H PHE* 2.8 30.4 + - - +
310H ILE* 3.9 16.6 - - - +
312H ARG* 1.3 77.1 - - - +
314H ARG* 1.3 57.2 + - - +
316H LEU* 4.6 0.2 - - - -
317H GLY 2.9 35.2 + - - +
319H PRO* 3.8 15.5 - - + -
306L LEU* 3.6 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 314 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310H ILE* 2.8 61.6 + - - +
311H TYR* 3.9 23.9 - - - +
312H ARG 3.2 0.2 - - - -
313H MET* 1.3 77.0 - - - +
315H GLN* 1.3 62.1 + - + +
305L SER* 3.8 38.1 - - - +
306L LEU* 3.5 13.6 - - + +
307L PRO* 3.7 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 315 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311H TYR* 3.1 56.6 + - + +
312H ARG* 2.9 32.7 + - - +
314H ARG* 1.3 82.0 - - + +
316H LEU* 1.3 62.7 + - + +
317H GLY 3.5 0.5 + - - -
307L PRO* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G TYR* 3.5 32.3 - - + +
68G ASN* 3.7 47.6 - - + +
69G LEU* 4.1 6.5 - - + +
312H ARG* 3.1 50.5 + - + +
313H MET 3.3 0.2 + - - -
315H GLN* 1.3 77.2 - - - +
317H GLY* 1.3 58.1 + - - +
310L ILE* 4.5 1.7 - - - +
311L TYR* 3.1 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 317 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G TYR* 2.7 28.7 + - - -
313H MET 2.9 13.4 + - - +
314H ARG 4.1 1.2 + - - -
315H GLN 3.3 3.4 + - - -
316H LEU* 1.3 79.9 - - - +
318H TYR* 1.3 65.1 + - - -
319H PRO* 3.7 1.0 - - - +
306L LEU* 4.9 1.1 - - - +
307L PRO* 3.3 26.9 - - - -
310L ILE* 4.5 6.1 - - - -
311L TYR* 4.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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