Contacts of the helix formed by residues 61 - 72 (chain A) in PDB entry 1R18
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 ALA 61 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.6 29.8 - - - +
50A PRO* 3.7 15.4 - - + +
60A SER* 1.3 75.7 - - - +
62A PRO* 1.3 62.0 - - + +
63A HIS* 3.2 27.6 - - + +
64A MET* 2.8 36.4 + - + +
65A HIS* 3.4 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.0 15.5 - - + -
14A ILE* 5.8 0.2 - - + -
17A LEU* 4.0 18.2 - - + -
32A MET* 3.5 13.5 - - + +
37A ARG* 3.6 41.7 - - - +
47A MET 3.6 10.1 - - - +
48A ASP* 3.4 16.8 - - - +
49A ALA 3.6 13.5 - - - +
60A SER 3.6 0.4 - - - -
61A ALA* 1.3 81.5 - - - +
63A HIS* 1.3 60.6 + - - +
65A HIS* 3.2 10.6 + - - +
66A ALA* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.3 5.5 - - + +
22A VAL* 3.8 27.1 - - + -
48A ASP* 2.9 37.4 + - - +
49A ALA* 5.7 0.2 - - - -
61A ALA* 3.0 18.9 + - + +
62A PRO* 1.3 78.6 - - - +
64A MET* 1.3 94.6 - - + +
66A ALA* 3.4 2.2 + - - +
67A PHE* 3.1 47.3 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 4.2 14.8 - - - -
61A ALA* 2.8 21.8 + - + +
63A HIS* 1.3 94.0 - - + +
65A HIS* 1.3 66.0 + - - +
67A PHE* 3.5 17.8 + - - +
68A ALA* 3.3 21.8 + - - +
197A MET* 5.9 7.4 - - + -
214A MET* 4.8 16.8 - - + +
216A VAL* 4.5 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A MET* 4.0 10.3 - - + -
37A ARG* 3.7 14.1 + - - -
59A ILE* 3.9 4.3 - - + -
60A SER* 3.4 35.2 + - - -
61A ALA 3.4 3.1 + - - -
62A PRO* 3.2 9.6 + - - +
64A MET* 1.3 78.3 - - - +
66A ALA* 1.3 63.0 + - - +
68A ALA* 3.4 6.3 + - - +
69A LEU* 3.1 29.5 + - + +
91A TYR* 3.2 35.3 - + + -
92A LEU* 4.2 26.8 - - + +
300A SAH 2.7 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 5.0 1.1 - - + -
22A VAL* 4.2 13.0 - - + +
23A ILE* 4.0 26.7 - - + -
28A VAL* 4.4 2.6 - - + +
32A MET* 4.0 15.9 - - + +
62A PRO 3.1 12.0 + - - +
63A HIS* 3.5 10.5 - - - +
64A MET 3.2 0.2 - - - -
65A HIS* 1.3 74.0 - - - +
67A PHE* 1.3 66.1 + - + +
69A LEU* 3.2 5.4 + - - +
70A GLU* 3.0 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.6 42.2 - - + -
63A HIS* 3.1 34.7 + + + +
64A MET* 3.8 19.5 - - - +
66A ALA* 1.3 77.7 - - - +
68A ALA* 1.3 57.9 + - - +
70A GLU* 3.4 6.5 + - + +
71A TYR* 3.0 54.5 + - + +
214A MET* 4.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET 3.3 10.6 + - - +
65A HIS* 3.7 9.0 - - - +
66A ALA 3.2 0.4 - - - -
67A PHE* 1.3 77.3 - - - +
69A LEU* 1.3 64.5 + - - +
71A TYR* 3.4 16.1 + - + +
72A LEU* 3.4 28.4 + - - +
92A LEU* 4.4 10.5 - - + -
96A PHE* 5.5 1.6 - - + -
162A HIS* 3.9 31.0 - - + +
185A ILE* 5.8 2.2 - - + -
197A MET* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.8 22.8 - - + +
31A ALA* 5.2 3.4 - - + -
32A MET* 3.7 33.0 - - + -
65A HIS* 3.1 19.2 + - + +
66A ALA 3.2 6.0 + - - +
68A ALA* 1.3 75.1 - - - +
70A GLU* 1.3 63.6 + - - +
72A LEU 3.3 3.6 + - - -
73A ARG* 3.0 23.2 + - - +
76A LEU* 4.2 13.8 - - + +
92A LEU* 4.1 9.6 - - + -
95A CYS* 4.2 23.3 - - + +
96A PHE* 3.5 35.2 - - + -
99A TYR* 5.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL 4.8 7.4 - - - +
23A ILE* 3.8 1.8 - - - +
24A ALA* 3.1 21.3 + - + +
25A SER* 3.1 40.8 + - - -
28A VAL* 3.4 16.0 - - + +
66A ALA 3.0 23.3 + - - +
67A PHE* 3.7 8.5 - - + +
68A ALA 3.3 0.2 - - - -
69A LEU* 1.3 77.4 - - - +
71A TYR* 1.3 65.8 + - + +
73A ARG* 2.7 63.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 3.0 49.8 + + + +
68A ALA* 3.6 13.2 - - + +
69A LEU 3.3 0.2 - - - -
70A GLU* 1.3 78.4 - - + +
72A LEU* 1.3 60.0 + - + +
73A ARG 3.9 0.5 + - - -
74A ASP 5.3 0.3 + - - -
75A HIS* 4.7 1.0 + - - -
183A ARG* 2.8 32.0 + - - +
185A ILE* 4.1 27.6 - - + -
197A MET* 4.7 9.4 - - + -
199A GLN* 4.9 2.9 - - - +
213A LEU* 3.8 47.5 + - + +
214A MET* 4.2 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA 3.4 15.8 + - - +
69A LEU 3.3 6.2 + - - +
70A GLU 3.2 0.6 - - - -
71A TYR* 1.3 76.3 - - - +
73A ARG* 1.3 63.9 + - - +
74A ASP 3.3 3.1 - - - -
75A HIS* 3.2 16.8 + - + -
76A LEU* 3.1 28.2 + - + +
82A ILE* 5.9 0.9 - - + -
96A PHE* 4.5 13.7 - - + -
160A ALA* 4.4 17.0 - - + -
161A ILE 4.6 3.1 - - - +
162A HIS* 4.2 25.8 - - + -
183A ARG* 3.5 45.3 - - + +
185A ILE* 3.6 19.5 - - + -
----------------------------------------------------------
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