Contacts of the strand formed by residues 53 - 62 (chain I) in PDB entry 1H64
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 VAL 53 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I GLU* 3.9 36.6 - - + +
47I MET 3.5 5.8 - - - -
48I ILE* 4.5 9.1 - - + +
51I GLY 4.3 0.2 - - - -
52I GLU* 1.3 72.3 - - - +
54I VAL* 1.3 62.4 + - - +
55I LYS 3.6 21.3 - - - +
56I ARG* 3.9 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I MET* 2.9 43.3 + - + +
49I GLN* 3.7 30.5 - - + +
52I GLU* 3.2 17.3 - - + +
53I VAL* 1.3 76.1 - - - +
55I LYS* 1.3 83.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H GLU* 4.2 16.6 + - - -
46I GLU* 3.3 4.0 - - - -
47I MET* 2.8 32.8 + - + +
53I VAL* 3.6 4.3 - - - +
54I VAL* 1.3 104.5 - - + +
56I ARG* 1.3 67.5 + - - +
57I TYR* 3.5 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I ASP* 5.8 4.3 - - - +
45I ALA 3.3 5.2 - - - +
46I GLU* 2.9 35.2 + - + -
53I VAL* 3.9 20.7 - - + +
55I LYS* 1.3 81.2 - - - +
57I TYR* 1.3 72.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H LEU* 4.2 14.8 - - + -
20H ILE* 3.5 23.8 - - + +
26H GLU* 5.5 0.9 + - - -
71H SER* 3.8 28.3 - - - +
27I PHE* 3.6 21.5 - + - -
44I ASP* 3.3 2.8 - - - +
45I ALA* 2.7 51.4 + - + +
47I MET* 3.1 39.1 - - + +
55I LYS* 3.5 23.5 + - + +
56I ARG* 1.3 80.9 - - - +
58I GLY* 1.3 61.5 + - - +
59I LYS 4.1 5.4 - - - +
60I ILE* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H SER* 5.0 1.0 + - - -
72H PRO 5.8 1.0 + - - -
43I ALA* 3.6 5.7 - - - +
44I ASP* 2.9 23.9 + - - -
57I TYR* 1.3 73.2 - - - +
59I LYS* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H GLU* 3.5 21.8 + - - -
8H VAL* 4.0 28.6 - - + +
11H ARG* 5.3 1.8 - - - +
71H SER* 2.5 30.4 + - - -
72H PRO* 3.1 25.2 + - + +
32I ILE* 4.1 15.9 - - + -
41I VAL* 4.1 10.8 - - + -
42I LEU 3.5 11.7 - - - +
43I ALA* 5.7 1.3 - - - -
57I TYR* 3.2 1.5 - - - -
58I GLY* 1.3 80.4 - - - +
60I ILE* 1.3 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H ILE* 4.5 4.9 - - + -
69H ALA* 3.7 24.9 - - + -
70H ILE 3.6 11.2 - - - +
71H SER* 4.0 7.2 - - - -
72H PRO* 4.7 0.4 - - - -
27I PHE* 3.7 29.2 - - + -
40I VAL 3.9 0.7 - - - +
41I VAL* 3.3 4.5 - - - +
42I LEU* 2.9 38.8 + - + +
45I ALA* 3.9 27.1 - - + -
57I TYR* 4.1 23.3 - - + -
59I LYS* 1.3 79.8 - - - +
61I VAL* 1.3 67.6 + - - +
62I ILE* 3.9 11.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H PRO* 3.9 31.2 - - + +
8H VAL* 3.8 35.0 - - + -
9H ILE* 4.3 15.7 - - + -
38H LEU* 5.4 9.4 - - + -
69H ALA* 3.0 6.1 - - - -
70H ILE* 2.8 45.7 + - + +
39I ASN* 5.2 2.5 - - + -
40I VAL 3.5 8.7 - - - +
41I VAL* 4.1 10.8 - - + -
60I ILE* 1.3 74.3 - - - +
62I ILE* 1.3 64.9 + - - +
63I ARG* 4.0 2.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H LEU* 3.7 12.8 - - + +
69H ALA* 4.2 9.9 - - + -
19I VAL* 4.4 9.2 - - + -
21I LEU* 4.4 13.5 - - + -
27I PHE* 3.4 44.0 - - + -
38I LEU 4.4 0.2 - - - +
39I ASN* 3.3 3.6 - - - +
40I VAL* 2.8 43.9 + - + +
42I LEU* 4.1 19.7 - - + -
60I ILE* 4.4 12.1 - - + +
61I VAL* 1.3 78.5 - - - +
63I ARG* 1.3 72.9 + - - +
64I GLY 3.4 0.2 + - - -
67I VAL* 4.2 15.9 - - + +
----------------------------------------------------------
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