Contacts of the helix formed by residues 61 - 71 (chain K) 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 VAL 61 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K HIS* 3.3 5.4 - - + +
60K GLU* 1.3 76.9 - - - +
62K SER* 1.3 61.8 + - - +
63K VAL 3.3 0.4 - - - -
64K PRO* 3.3 14.7 - - - +
65K TYR* 4.1 9.9 + - - +
320L PRO* 4.4 27.9 - - + +
321L GLY* 5.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 62 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K ALA* 4.5 3.6 + - - +
34K GLY* 3.8 18.5 - - - -
35K PRO* 4.2 7.8 - - - +
57K PHE* 3.5 29.6 - - - +
59K HIS* 3.3 17.8 + - - +
60K GLU 3.1 1.4 + - - -
61K VAL* 1.3 77.9 - - - +
63K VAL* 1.3 59.4 + - - +
65K TYR* 3.2 7.0 + - - +
66K ALA* 2.8 32.8 + - - +
320L PRO* 6.0 0.9 - - - -
321L GLY* 4.2 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K ASP 3.3 26.2 - - - +
10K ARG* 4.1 20.0 - - - +
11K THR 4.5 8.1 - - - +
12K LEU* 4.8 12.8 - - + -
57K PHE* 4.4 10.5 - - + -
59K HIS 4.8 1.3 - - - +
60K GLU* 3.2 9.3 + - + +
62K SER* 1.3 75.8 - - - +
64K PRO* 1.3 72.9 - - + +
66K ALA* 3.7 5.3 - - - +
67K MET* 3.1 23.8 + - + +
84K PHE* 5.1 17.0 - - + -
85K ARG 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 64 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60K GLU 3.8 7.0 - - - +
61K VAL* 3.3 17.3 - - - +
63K VAL* 1.3 95.0 - - + +
65K TYR* 1.3 56.5 + - - +
67K MET* 3.2 8.7 + - + +
68K ASN* 2.9 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K ALA* 3.6 29.4 - - + -
61K VAL 4.1 9.2 + - - +
62K SER* 3.2 9.7 + - - +
64K PRO* 1.3 76.6 - - - +
66K ALA* 1.3 67.1 + - - +
68K ASN* 3.3 11.7 + - - +
69K LEU* 2.9 35.5 + - + +
313L MET* 3.1 28.1 - - + +
316L LEU* 3.5 35.4 - - + -
317L GLY 2.6 25.9 + - - -
318L TYR 4.8 0.9 - - - -
319L PRO* 3.6 25.1 - - + +
320L PRO* 4.4 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K LEU* 5.9 2.9 - - + -
30K PHE* 4.3 13.2 - - + -
33K ALA* 3.7 16.7 - - + +
57K PHE* 3.8 29.8 - - + -
62K SER 2.8 20.3 + - - +
63K VAL* 3.7 4.5 - - - +
65K TYR* 1.3 72.3 - - - +
67K MET* 1.3 55.0 + - - +
69K LEU* 3.1 0.8 + - - -
70K LEU* 2.7 38.4 + - - +
82K ILE* 4.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K VAL* 3.1 15.3 + - + +
64K PRO* 3.4 11.4 - - + +
66K ALA* 1.3 77.0 - - - +
68K ASN* 1.3 68.1 + - - +
71K ASN* 3.1 60.4 + - - +
82K ILE* 3.9 35.1 - - + +
83K GLN* 4.4 0.4 - - - -
84K PHE* 4.1 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64K PRO* 2.9 23.6 + - - +
65K TYR* 3.3 12.9 + - - +
67K MET* 1.3 82.3 - - - +
69K LEU* 1.3 62.4 + - - +
71K ASN 4.8 2.9 + - - +
316L LEU* 3.9 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K GLN* 4.7 3.1 - - + -
33K ALA* 4.3 18.6 - - + +
65K TYR* 2.9 23.1 + - + +
66K ALA* 3.9 2.2 - - - +
68K ASN* 1.3 79.7 - - - +
70K LEU* 1.3 82.9 + - + +
71K ASN 3.7 1.7 + - - +
73K ILE* 4.1 11.3 - - - +
309L PHE* 4.1 30.3 - - + +
312L ARG* 4.4 9.0 - - + -
313L MET* 3.6 34.8 - - + +
316L LEU* 4.2 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K LEU* 3.8 30.1 - - + +
30K PHE* 3.6 50.0 - - + +
32K GLN* 5.7 1.6 - - + +
33K ALA* 4.4 13.5 - - + -
66K ALA* 2.7 19.1 + - + +
69K LEU* 1.3 99.0 - - + +
71K ASN* 1.3 59.9 + - - +
73K ILE* 3.2 27.0 + - + +
80K ILE* 3.5 18.7 - - + +
82K ILE* 3.6 10.8 - - + -
309L PHE* 5.6 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 71 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K MET* 3.1 41.9 + - - +
68K ASN 4.8 2.5 + - - +
69K LEU 3.7 2.7 - - - +
70K LEU* 1.3 76.5 - - - +
72K GLY* 1.3 67.2 + - - +
73K ILE* 3.4 2.1 + - - +
80K ILE 3.5 2.9 - - - +
81K LYS* 4.1 1.7 - - - -
82K ILE* 3.2 42.4 + - + +
----------------------------------------------------------
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