Contacts of the helix formed by residues 28 - 41 (chain A) in PDB entry 6R7Y
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 LYS 28 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP 5.5 0.9 - - - +
27A VAL* 1.3 84.5 - - - +
29A GLU* 1.3 65.7 + - - +
30A GLU* 3.3 8.0 + - + +
31A THR* 3.6 9.4 + - - +
32A LYS* 3.4 15.9 + - - +
145A GLY* 2.4 41.1 + - - +
146A TYR* 3.7 27.1 + - + +
147A PRO* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL 4.2 4.0 - - - +
28A LYS* 1.3 73.8 - - - +
30A GLU* 1.3 64.7 + - - +
31A THR 3.3 0.2 - - - -
32A LYS* 3.3 34.8 + - - +
33A GLU* 3.1 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 3.3 5.6 - - + +
29A GLU* 1.3 79.0 - - - +
31A THR* 1.3 57.1 + - - +
33A GLU* 3.5 5.2 + - - +
34A TRP* 2.9 31.5 + - + +
144A PRO* 4.0 30.3 - - + +
145A GLY* 5.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.5 11.2 - - + -
28A LYS* 3.6 15.0 + - - +
29A GLU 3.3 0.2 - - - -
30A GLU* 1.3 75.8 - - - +
32A LYS* 1.3 59.6 + - - +
34A TRP* 3.9 14.0 - - + +
35A LEU* 2.9 30.6 + - + +
143A ILE* 3.9 24.0 - - + -
144A PRO* 3.2 18.1 + - - -
145A GLY* 4.8 0.2 - - - -
146A TYR* 4.1 20.1 - - + -
161A LEU* 5.1 11.7 - - + -
166A ILE* 5.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.1 20.4 - - + -
24A ALA 5.7 0.9 - - - -
25A GLN 5.6 2.6 + - - -
27A VAL* 3.8 30.5 + - + -
28A LYS 3.4 7.9 + - - +
29A GLU* 3.3 38.9 + - - +
31A THR* 1.3 78.0 - - - +
33A GLU* 1.3 62.8 + - - +
35A LEU* 3.4 5.4 + - - +
36A LYS* 2.9 29.5 + - - +
67A GLN* 5.0 15.2 + - - +
68A ASN* 5.3 7.3 - - - +
70A TYR* 3.8 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 3.1 31.7 + - + +
30A GLU* 4.1 4.3 - - - +
32A LYS* 1.3 77.6 - - - +
34A TRP* 1.3 60.8 + - - +
36A LYS* 3.8 18.9 - - - +
37A ASN* 2.9 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 2.9 21.3 + - + +
31A THR* 3.9 16.4 - - + +
33A GLU* 1.3 77.6 - - - +
35A LEU* 1.3 84.9 + - + +
37A ASN* 3.5 6.7 + - + +
38A ARG* 3.1 31.9 + - + +
140A GLU* 3.5 33.5 + - + +
143A ILE* 4.1 28.5 - - + -
144A PRO* 4.0 33.2 - - + +
151A LEU* 4.7 5.2 - - + -
157A LEU* 3.6 42.8 - - + -
161A LEU* 5.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 5.5 8.3 - - + -
23A LEU* 4.5 28.0 - - + -
31A THR* 2.9 20.3 + - + +
32A LYS* 3.8 4.3 - - - +
34A TRP* 1.3 88.8 - - + +
36A LYS* 1.3 62.4 + - - +
38A ARG* 3.1 8.7 + - + +
39A ILE* 3.1 43.6 + - + +
52A PHE* 5.7 7.2 - - + -
70A TYR* 5.9 2.2 - - + -
135A LEU* 5.3 7.6 - - + -
157A LEU* 5.8 4.3 - - + -
158A LEU* 6.0 3.6 - - + -
161A LEU* 4.2 26.2 - - + -
167A VAL* 5.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS 2.9 18.5 + - - +
33A GLU* 3.9 19.9 + - - +
35A LEU* 1.3 75.6 - - - +
37A ASN* 1.3 59.2 + - - +
39A ILE* 3.4 5.7 + - - +
40A ILE* 3.2 51.6 + - + +
52A PHE* 3.7 41.2 + - + -
54A PRO* 4.9 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 2.9 27.1 + - - +
34A TRP* 3.8 7.1 - - + +
36A LYS* 1.3 79.0 - - - +
38A ARG* 1.3 62.7 + - + +
39A ILE 3.3 0.2 - - - -
40A ILE* 4.4 3.5 - - - +
41A ALA* 3.3 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 3.1 37.2 + - + +
35A LEU* 3.1 8.7 + - + +
37A ASN* 1.3 81.5 - - + +
39A ILE* 1.3 59.6 + - - +
41A ALA* 5.9 0.4 - - - -
46A GLY* 2.8 31.2 + - - -
47A GLY* 3.6 8.6 - - - -
48A ALA 3.4 17.3 + - - -
135A LEU* 3.9 31.1 - - + +
136A ARG 2.7 30.1 + - - +
137A ALA* 4.6 0.6 - - - +
138A LYS 5.1 1.2 - - - +
140A GLU* 3.4 31.7 + - - -
157A LEU* 4.3 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 4.5 12.1 - - + -
35A LEU* 3.1 34.4 + - + +
36A LYS 3.4 4.0 + - - +
37A ASN 3.3 0.2 - - - -
38A ARG* 1.3 80.9 - - - +
40A ILE* 1.3 60.8 + - - +
41A ALA 3.3 0.4 - - - -
48A ALA* 3.5 5.7 + - + -
49A GLN 2.9 26.2 + - - -
50A LEU* 3.1 36.3 + - + +
52A PHE* 3.8 40.4 - - + -
72A VAL* 4.7 4.5 - - + -
132A LEU* 4.3 24.9 - - + -
135A LEU* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 3.2 48.4 + - + +
37A ASN* 5.4 3.1 - - - +
39A ILE* 1.3 77.0 - - + +
41A ALA* 1.3 65.1 + - - +
42A LYS* 3.7 2.9 + - - +
49A GLN* 3.6 12.0 - - - +
50A LEU 3.8 12.3 - - - +
51A LEU* 5.9 2.7 - - + -
52A PHE* 4.0 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 3.3 21.4 + - - +
38A ARG* 5.9 0.7 - - - -
39A ILE 3.3 1.6 - - - -
40A ILE* 1.3 79.2 - - - +
42A LYS* 1.3 59.4 + - - +
45A ASP* 4.7 12.8 - - + +
47A GLY* 3.9 12.1 - - - +
48A ALA 2.8 10.7 + - - -
49A GLN 2.7 28.2 + - - -
----------------------------------------------------------
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