Contacts of the helix formed by residues 45 - 59 (chain A) in PDB entry 6XWQ
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 ILE 45 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.4 38.6 - - + -
41A VAL* 3.2 19.8 + - + +
44A TYR* 1.3 83.1 - - + +
46A LYS* 1.3 67.2 + - - +
47A PRO 3.2 2.5 - - - -
48A PHE* 2.8 34.8 + - + +
212A PHE* 4.5 15.0 - - + +
213A ALA* 3.5 31.6 - - + +
216A ALA* 5.2 1.8 - - + -
217A TYR* 5.8 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL 3.0 10.7 + - - +
42A LYS* 3.2 46.0 - - + +
45A ILE* 1.3 76.5 - - - +
47A PRO* 1.3 64.6 - - - +
49A GLY* 3.0 6.0 + - - +
50A ASP* 2.9 39.3 + - + +
213A ALA* 5.0 2.5 - - - -
214A LEU* 5.5 2.1 - - + +
217A TYR* 4.3 39.4 - - + +
137C LEU* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS 4.0 3.4 - - - +
43A THR 3.6 17.5 - - - +
44A TYR 3.3 20.6 - - - +
46A LYS* 1.3 96.8 - - + +
48A PHE* 1.3 60.4 + - + +
50A ASP* 4.3 3.1 - - + -
51A LEU* 2.9 30.5 + - - +
133C VAL* 4.5 22.7 - - + -
137C LEU* 3.4 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR 5.1 8.1 - - - -
45A ILE* 2.8 35.8 + - + +
47A PRO* 1.3 77.4 - - + +
49A GLY* 1.3 56.9 + - - +
51A LEU* 3.3 12.4 + - + +
52A PHE* 2.9 27.8 + - - +
206A TYR* 3.8 19.5 + - - +
209A ILE* 4.5 27.4 - - + +
210A GLY* 4.8 1.3 - - - -
213A ALA* 3.6 10.5 - - + -
137C LEU* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS 3.0 6.5 + - - -
48A PHE* 1.3 80.4 - - - +
50A ASP* 1.3 56.3 + - - +
52A PHE* 3.2 4.7 + - - +
53A VAL* 2.9 33.1 + - - +
210A GLY 3.8 5.2 - - - -
213A ALA* 3.3 16.5 - - - +
214A LEU* 3.7 27.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 2.9 34.0 + - + +
47A PRO* 3.8 5.4 - - + +
49A GLY* 1.3 74.9 - - - +
51A LEU* 1.3 59.0 + - - +
53A VAL* 3.3 9.8 + - - +
54A ARG* 2.9 48.1 + - - +
214A LEU* 4.5 1.5 - - - +
134C GLN* 4.9 7.1 + - - +
137C LEU* 3.7 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO 2.9 18.1 + - - +
48A PHE* 3.6 11.0 - - + +
50A ASP* 1.3 76.6 - - - +
52A PHE* 1.3 59.5 + - - +
54A ARG* 3.3 5.9 + - - +
55A LEU* 2.9 39.4 + - + +
206A TYR* 3.2 27.8 - - + +
136C LEU* 6.5 0.7 - - + -
137C LEU* 4.1 22.8 - - + +
140C VAL* 3.6 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE 2.9 13.6 + - - +
49A GLY 3.2 6.3 + - - +
51A LEU* 1.3 77.2 - - - +
53A VAL* 1.3 57.7 + - + +
55A LEU* 3.3 4.3 + - - +
56A LEU* 2.9 51.0 + - + +
203A VAL* 3.9 13.5 - - + -
204A MET* 5.1 0.9 - - + -
206A TYR* 4.0 22.9 - + + -
207A ALA* 3.5 26.0 - - + -
210A GLY* 3.9 27.4 - - - -
211A VAL* 4.3 16.4 - - + -
214A LEU* 4.3 16.6 - - + -
277A THR* 3.3 32.1 - - - -
278A ARG* 6.2 0.2 - - + -
359A PRO* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 2.9 20.7 + - - +
50A ASP* 3.3 11.0 + - - +
52A PHE* 1.3 77.5 - - + +
54A ARG* 1.3 58.3 + - + +
56A LEU* 3.3 6.5 + - - +
57A LYS* 2.9 51.1 + - - +
214A LEU* 3.7 28.7 - - + -
278A ARG* 6.0 0.7 - - - +
359A PRO* 4.4 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 2.9 38.1 + - - +
51A LEU* 3.7 1.8 - - - +
52A PHE 3.3 0.2 - - - -
53A VAL* 1.3 77.7 - - + +
55A LEU* 1.3 61.8 + - - +
57A LYS* 3.2 17.9 + - - +
58A MET* 2.9 23.0 + - - +
134C GLN* 5.0 6.2 - - - +
137C LEU* 3.1 30.9 + - - -
138C ASN* 4.0 25.8 + - - +
140C VAL* 3.2 33.5 + - + +
141C PRO* 3.7 7.2 - - - +
142C THR* 2.9 33.9 + - - +
155C PRO* 6.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 2.9 29.9 + - + +
52A PHE* 3.4 8.1 - - - +
54A ARG* 1.3 75.3 - - - +
56A LEU* 1.3 62.8 + - - +
58A MET* 3.1 41.1 + - + +
59A LEU* 3.5 14.4 - - - +
203A VAL* 4.3 25.8 - - + -
206A TYR* 4.1 32.8 - - + -
140C VAL* 3.7 24.9 - - + -
158C PHE* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 2.9 49.9 + - + +
53A VAL* 3.3 4.7 + - - +
55A LEU* 1.3 76.3 - - - +
57A LYS* 1.3 58.2 + - - +
59A LEU* 3.9 21.9 + - + +
60A VAL* 4.5 0.3 - - - +
200A VAL* 5.4 1.6 - - + -
203A VAL* 3.8 18.4 - - + -
204A MET* 4.5 4.0 - - + -
277A THR* 3.6 4.3 - - - +
279A SER* 3.1 31.4 - - - +
281A SER 5.6 0.7 - - - +
282A GLY* 3.8 29.5 + - - +
357A GLY 4.8 2.6 - - - +
358A VAL* 3.7 13.6 - - - +
359A PRO* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 2.9 41.3 + - - +
54A ARG* 3.2 15.2 + - - +
56A LEU* 1.3 76.1 - - - +
58A MET* 1.3 64.4 + - - +
59A LEU 3.1 2.5 + - - -
60A VAL* 3.3 19.9 - - + +
358A VAL* 3.6 36.1 - - + -
359A PRO 5.3 1.1 - - - -
142C THR* 2.8 42.6 + - + +
143C ASN* 4.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ARG 2.9 8.0 + - - +
55A LEU* 3.1 35.9 + - + +
57A LYS* 1.3 77.6 - - - +
59A LEU* 1.3 78.7 + - + +
62A PRO* 3.4 13.5 - - - +
199A ILE* 4.7 7.9 - - + -
203A VAL* 5.1 1.8 - - + -
141C PRO* 3.2 39.7 - - + +
142C THR 3.3 10.0 + - - -
143C ASN* 5.0 0.2 - - - +
144C PRO* 3.4 19.5 - - + +
158C PHE* 4.1 12.8 - - + -
159C PHE* 3.8 29.4 - - + -
162C ILE* 4.8 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU 3.5 14.3 + - - +
56A LEU* 3.9 12.7 + - + +
57A LYS 3.1 1.0 - - - -
58A MET* 1.3 97.6 - - + +
60A VAL* 1.3 58.4 + - - +
61A MET 3.9 0.2 - - - -
62A PRO* 4.5 4.5 - - - -
63A ILE* 3.1 35.1 - - + +
196A MET* 4.0 18.2 - - + -
199A ILE* 3.6 32.3 - - + -
200A VAL* 3.6 24.2 - - + -
203A VAL* 3.8 24.0 - - + -
281A SER* 3.4 12.1 + - - +
159C PHE* 5.3 0.2 - - + -
----------------------------------------------------------
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