Contacts of the helix formed by residues 51 - 64 (chain A) in PDB entry 4XQ2
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 ASN 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A HIS* 2.8 28.9 + - - +
30A VAL* 4.9 0.8 - - - +
31A SER 4.4 5.5 + - - -
34A TYR* 3.6 10.0 + - - -
44A TYR* 4.3 0.2 - - - -
47A GLY* 4.2 4.1 - - - +
50A GLU* 1.3 76.3 - - - +
52A PRO* 1.3 72.0 - - - +
53A THR* 3.0 12.3 + - - -
54A ARG* 2.9 53.5 + - + +
55A GLU* 3.0 30.9 + - - +
234A ALA* 4.2 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A HIS* 3.8 40.4 - - + +
34A TYR* 3.7 13.9 - - + +
44A TYR* 3.6 23.6 - - + +
51A ASN* 1.3 82.2 - - - +
53A THR* 1.3 58.2 + - - +
55A GLU* 3.2 13.3 + - - +
56A GLU* 3.0 41.6 + - - +
21C THR* 4.1 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PRO 3.6 10.7 + - - -
28A ILE* 3.7 3.9 - - + -
29A HIS* 2.9 33.8 + - - +
51A ASN* 3.0 10.1 + - - +
52A PRO* 1.3 75.3 - - - +
54A ARG* 1.3 67.4 + - - +
56A GLU* 3.3 14.7 + - - +
57A LEU* 3.3 20.1 + - - +
234A ALA* 3.6 24.2 - - - +
237A CYS* 3.9 10.1 - - + -
238A PHE* 4.2 13.5 - - + +
241A ARG* 6.4 0.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
47A GLY 3.0 25.1 + - - -
48A ARG 3.9 5.5 + - - -
49A GLY 2.8 32.3 + - - -
50A GLU* 3.7 1.6 - - - +
51A ASN* 2.9 37.2 + - - +
53A THR* 1.3 75.8 - - - +
55A GLU* 1.3 67.6 + - - +
57A LEU* 3.2 4.7 + - - +
58A GLU* 3.0 32.3 + - - +
72A VAL* 3.4 22.2 - - + -
222A ARG* 5.5 1.0 - - - +
225A ARG* 3.1 39.7 - - - +
231A VAL* 4.5 7.9 - - - +
232A PRO* 4.0 23.1 + - - -
234A ALA* 6.3 0.2 - - - -
237A CYS* 3.7 19.4 - - - +
206B LEU* 5.5 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 6.1 3.6 - - - -
43A ARG* 3.5 15.6 + - - -
44A TYR* 2.4 41.5 + - - -
49A GLY 5.2 0.5 - - - +
50A GLU* 4.2 4.5 - - - -
51A ASN 3.0 24.5 + - - +
52A PRO* 3.2 9.9 + - - +
54A ARG* 1.3 82.2 + - + +
56A GLU* 1.3 56.8 + - + +
58A GLU* 3.4 15.6 + - - +
59A GLU* 2.9 33.4 + - - +
222A ARG* 5.8 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY 4.3 0.5 - - - +
14A GLY* 3.5 13.1 - - - +
16A ARG* 3.5 38.8 - - + +
26A PRO* 3.2 32.3 - - + +
27A PRO* 4.8 1.0 - - - +
29A HIS* 4.8 6.2 + - - -
52A PRO* 3.0 34.3 + - - +
53A THR* 3.7 15.7 + - - +
54A ARG 3.3 0.2 - - - -
55A GLU* 1.3 77.2 - - + +
57A LEU* 1.3 57.3 + - - +
59A GLU* 3.4 8.9 + - - +
60A CYS* 2.8 29.5 + - - +
241A ARG* 4.8 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A THR 3.3 9.1 + - - +
54A ARG* 3.2 9.3 + - - +
56A GLU* 1.3 80.0 - - - +
58A GLU* 1.3 56.7 + - - +
60A CYS* 3.1 6.3 + - - +
61A LEU* 2.8 31.7 + - + +
72A VAL* 3.8 25.6 - - + -
237A CYS* 4.0 29.4 - - + +
240A VAL* 3.9 31.0 - - + -
241A ARG* 4.0 20.7 - - + +
244A LEU* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ARG* 3.0 26.4 + - - +
55A GLU* 3.5 20.0 + - - +
57A LEU* 1.3 75.4 - - - +
59A GLU* 1.3 58.6 + - - +
61A LEU* 3.3 3.2 + - - +
62A ALA* 2.9 27.4 + - - +
70A ALA* 3.2 29.6 - - - +
71A THR* 3.3 4.0 - - - -
72A VAL* 3.0 33.5 + - + +
222A ARG* 3.4 21.4 + - - +
225A ARG* 2.7 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY* 5.4 0.2 - - - -
14A GLY* 3.1 32.7 + - - +
16A ARG* 3.1 53.5 + - - +
55A GLU* 2.9 14.3 + - - +
56A GLU* 3.7 7.9 - - - +
58A GLU* 1.3 76.1 - - - +
60A CYS* 1.3 61.7 + - - +
62A ALA* 3.6 5.0 + - - +
63A GLY* 3.0 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.9 17.1 - - - +
10A LEU* 4.3 3.8 - - - -
13A GLY* 3.3 24.6 - - - +
14A GLY* 4.3 0.2 - - - -
56A GLU 2.8 13.0 + - - +
57A LEU* 3.3 11.2 - - + +
59A GLU* 1.3 76.9 - - - +
61A LEU* 1.3 62.7 + - - +
63A GLY* 3.1 11.1 + - - -
64A LEU* 3.2 16.9 + - - +
241A ARG* 3.7 32.3 - - - +
244A LEU* 4.3 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 2.8 31.1 + - + +
58A GLU* 3.8 4.7 - - - +
60A CYS* 1.3 68.8 - - - +
62A ALA* 1.3 65.9 + - - +
64A LEU* 3.1 32.9 + - + +
65A GLU* 3.8 4.3 + - - +
70A ALA* 4.4 6.7 - - + -
72A VAL* 3.6 31.0 - - + -
178A PRO* 5.8 2.0 - - + -
193A TYR* 6.0 2.9 - - + -
195A THR* 4.3 8.7 - - + -
199A ILE* 4.3 17.3 - - + -
209A ALA* 3.7 19.1 - - + -
211A VAL* 4.3 16.2 - - + +
244A LEU* 3.6 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU 2.9 20.0 + - - +
59A GLU* 4.0 6.1 - - - +
61A LEU* 1.3 73.1 - - - +
63A GLY* 1.3 62.5 + - - +
65A GLU* 3.0 7.8 + - - -
67A ALA* 2.9 41.8 + - - +
68A PRO 4.5 1.8 - - - +
69A PHE* 3.5 27.6 - - - +
70A ALA* 3.8 1.9 - - + +
211A VAL* 4.0 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 2.2 43.7 + - - -
13A GLY* 6.2 2.0 - - - -
59A GLU 3.0 15.4 + - - -
60A CYS* 3.1 6.9 + - - -
62A ALA* 1.3 77.5 - - - +
64A LEU* 1.3 49.6 - - - +
65A GLU 3.1 0.9 + - - -
66A ARG* 3.1 8.2 + - - +
67A ALA 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.8 11.1 - - + -
9A ARG* 3.0 46.0 + - + +
10A LEU* 3.6 36.8 - - + -
60A CYS* 3.5 14.1 - - - +
61A LEU* 3.1 22.0 + - + +
63A GLY* 1.3 75.8 - - - +
65A GLU* 1.3 57.0 + - + +
178A PRO* 3.9 29.6 - - + -
182A GLN* 2.8 22.7 + - - +
244A LEU* 3.9 18.4 - - + -
247A LEU* 4.8 0.4 - - + -
----------------------------------------------------------
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