Contacts of the helix formed by residues 57 - 70 (chain D) in PDB entry 1RHP
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 57 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D LEU* 5.6 0.4 - - + -
54D ASP* 2.7 33.2 + - + +
55D LEU 3.6 0.6 - - - -
56D GLN* 1.3 71.1 - - - +
58D PRO* 1.3 72.0 - - + +
59D LEU* 3.9 32.5 - - + +
60D TYR* 3.3 8.3 - - + -
61D LYS* 3.1 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLN 4.0 3.8 - - - +
57D ALA* 1.3 84.5 - - + +
59D LEU* 1.3 54.9 + - + +
61D LYS* 2.8 47.8 + - + +
62D LYS* 3.8 3.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D THR 3.9 21.8 - - - +
17D SER* 3.9 19.7 - - - +
19D VAL* 3.6 33.4 - - + +
21D PRO* 5.3 3.0 - - + +
53D LEU* 4.2 15.9 - - + -
57D ALA* 3.9 21.8 - - + -
58D PRO* 1.3 77.1 - - + +
60D TYR* 1.3 59.0 + - + +
62D LYS* 3.3 8.9 + - - +
63D ILE* 2.9 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 4.9 2.5 - - + -
68C LEU* 3.3 35.9 - - + +
27D LEU* 4.7 2.7 - - + -
41D LEU* 3.7 28.9 - - + -
53D LEU* 4.7 6.1 - - + -
54D ASP 4.8 2.2 - - - -
55D LEU 4.1 21.2 + - - -
56D GLN* 4.7 0.6 - - - -
57D ALA* 3.3 26.9 - - + -
58D PRO 2.9 2.6 + - - -
59D LEU* 1.3 73.9 - - - +
61D LYS* 1.3 87.8 + - + +
62D LYS 3.3 0.2 - - - -
63D ILE* 3.6 14.1 - - + -
64D ILE* 2.9 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLN* 4.7 5.2 - - - +
57D ALA 3.1 23.1 - - - +
58D PRO* 2.8 30.0 + - + +
60D TYR* 1.3 112.6 + - + +
62D LYS* 1.3 62.7 + - - +
64D ILE* 4.6 1.0 - - - +
65D LYS* 3.2 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PRO* 3.9 27.0 - - + +
58D PRO 3.8 2.9 + - - +
59D LEU* 3.3 9.2 + - - +
61D LYS* 1.3 76.7 - - - +
63D ILE* 1.3 55.0 + - - +
65D LYS* 2.6 37.6 + - + +
66D LYS* 3.0 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D VAL* 4.0 9.2 - - + -
21D PRO* 3.9 17.0 - - + +
24D ILE* 3.5 28.7 - - + -
27D LEU* 3.6 25.8 - - + -
53D LEU* 3.5 28.3 - - + -
59D LEU* 2.9 29.9 + - + +
60D TYR* 3.6 5.2 - - - +
61D LYS 3.5 0.2 - - - -
62D LYS* 1.3 74.4 - - - +
64D ILE* 1.3 63.9 + - - +
66D LYS* 3.9 5.4 - - - +
67D LEU* 3.0 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 5.8 0.2 - - + -
29C VAL* 4.6 9.9 - - + -
60C TYR* 5.0 3.1 - - + -
64C ILE* 3.6 39.0 - - + -
68C LEU* 5.4 0.4 - - + -
27D LEU* 3.8 26.5 - - + -
29D VAL* 5.0 5.6 - - + -
60D TYR* 2.9 39.7 + - + +
61D LYS 4.8 1.1 - - - +
62D LYS 3.0 0.2 + - - -
63D ILE* 1.3 72.0 - - - +
65D LYS* 1.3 56.6 + - + +
67D LEU* 3.4 6.4 + - + -
68D LEU* 2.9 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D LYS* 3.2 29.2 + - - +
62D LYS* 2.6 18.2 + - + +
64D ILE* 1.3 67.0 - - + +
66D LYS* 1.3 61.7 + - + +
67D LEU 3.1 1.3 - - - -
68D LEU* 2.8 15.3 + - + -
69D GLU* 2.6 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LYS* 4.8 12.0 - - - +
21D PRO* 4.0 38.5 - - + +
22D ARG* 4.6 18.6 - - + +
62D LYS* 3.0 35.5 + - + +
63D ILE* 4.1 4.0 - - - +
65D LYS* 1.3 76.5 - - + +
67D LEU* 1.4 59.0 + - + +
69D GLU* 3.3 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 3.6 27.7 - - + +
30C ILE 4.3 0.5 - - - +
31C LYS* 3.9 28.2 - - + +
32C ALA 4.7 0.7 + - - -
39C ALA* 3.2 20.4 - - - +
21D PRO 5.6 1.6 - - - +
24D ILE* 3.9 25.6 - - + +
25D THR 3.6 22.4 - - - +
27D LEU* 3.9 17.0 - - + -
63D ILE* 3.0 43.9 + - + +
64D ILE* 3.8 3.1 - - - +
66D LYS* 1.4 78.1 - - + +
68D LEU* 1.3 62.6 + - - +
69D GLU 4.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 3.7 17.9 - - + -
39C ALA* 3.7 11.9 - - + +
41C LEU* 3.6 29.8 - - + -
55C LEU* 3.7 25.9 - - + +
60C TYR* 3.5 31.0 - - + +
64D ILE* 2.9 36.4 + - + +
65D LYS* 2.8 5.2 + - + -
67D LEU* 1.3 81.0 - - - +
69D GLU* 1.4 74.3 + - - +
70D SER 3.4 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LYS* 6.0 0.3 - - - -
65D LYS* 2.6 46.4 + - - +
66D LYS* 3.3 18.7 - - - +
67D LEU 4.9 0.6 - - - -
68D LEU* 1.4 90.1 - - - +
70D SER* 1.3 67.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LYS* 5.9 7.2 - - - -
32C ALA* 3.7 35.4 + - - +
37C PRO 4.3 9.9 - - - -
38C THR* 3.8 10.4 - - - +
39C ALA* 3.8 7.4 + - - +
68D LEU 3.4 11.6 + - - +
69D GLU* 1.3 77.9 - - - +
----------------------------------------------------------
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