Contacts of the strand formed by residues 68 - 79 (chain S) in PDB entry 3HOU
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 68 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1445M ILE* 3.7 27.6 - - + -
11S ILE 3.6 0.7 - - - +
12S THR* 3.2 4.7 + - - -
13S LEU* 2.9 31.2 + - - +
18S PHE* 3.5 21.2 - - + -
60S ARG 3.1 10.8 - - - +
61S ILE* 4.0 3.4 - - + +
62S LEU* 4.3 2.2 - - - -
67S SER* 1.3 76.4 - - - +
69S GLU* 1.3 60.4 + - - +
70S PHE* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M LEU 5.1 6.7 - - - +
10S ASN* 3.9 33.5 + - + +
11S ILE 3.3 8.3 - - - +
12S THR* 3.9 13.5 + - - +
58S ARG 4.7 0.2 - - - +
59S GLY* 3.2 1.5 - - - -
60S ARG* 2.6 41.4 + - + +
62S LEU* 3.8 21.3 - - + +
68S ALA* 1.3 74.8 - - - +
70S PHE* 1.3 62.4 + - - +
71S ASN 4.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1445M ILE* 3.2 35.4 - - + -
1447M GLU* 5.9 2.5 - - + -
10S ASN* 3.3 6.1 - - - +
11S ILE 2.9 38.9 + - - +
13S LEU* 3.8 23.8 - - + -
22S MET* 3.9 25.4 - - + -
26S LEU* 3.6 34.3 - - + -
56S ILE* 3.9 21.5 - - + +
57S GLN 3.9 11.4 - - - -
58S ARG 5.2 0.4 - - - -
59S GLY* 3.2 22.2 - - - -
68S ALA* 4.0 8.5 - - + -
69S GLU* 1.3 75.6 - - - +
71S ASN* 1.3 60.8 + - - +
72S VAL* 3.5 9.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 71 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P SER* 5.6 1.0 - - - -
8S SER* 3.8 21.1 + - - -
9S LEU 3.3 15.3 + - - +
10S ASN* 3.5 21.3 + - - +
55S ASP 4.0 0.2 - - - +
56S ILE 3.9 8.0 + - - +
57S GLN* 2.5 40.5 + - - +
58S ARG 5.6 1.2 + - - -
69S GLU 4.3 0.8 + - - -
70S PHE* 1.3 72.8 - - - +
72S VAL* 1.3 59.7 + - - +
73S LYS* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S SER* 3.2 3.9 - - - -
9S LEU* 2.7 40.4 + - - +
11S ILE* 4.4 22.9 - - + -
26S LEU* 5.2 11.0 - - + -
27S LYS* 6.1 1.3 - - - +
30S LEU* 3.7 27.1 - - + -
54S ILE* 3.6 28.5 - - + -
55S ASP 3.5 8.1 - - - +
56S ILE* 4.9 6.7 - - + +
70S PHE* 4.3 16.6 - - + +
71S ASN* 1.3 68.5 - - - +
73S LYS* 1.3 63.1 + - - +
74S TYR* 3.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P HIS* 3.5 57.1 + - + +
7S LEU 4.1 1.3 - - - -
8S SER* 4.2 5.2 - - - -
54S ILE* 3.8 2.1 - - - +
55S ASP* 3.0 51.1 + - + +
57S GLN* 3.8 24.4 - - - +
71S ASN* 3.3 26.2 + - - +
72S VAL* 1.3 71.8 - - - +
74S TYR* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P THR* 3.3 14.2 + - - -
40P HIS* 2.7 15.2 + - - -
6S ASP 4.0 0.2 - - - -
7S LEU* 2.6 62.1 + - + +
8S SER* 3.4 13.2 - - - -
9S LEU* 4.6 0.7 - - + -
30S LEU* 3.9 15.9 - - + -
34S VAL* 2.9 53.2 - - + +
45S ILE* 3.3 6.9 - - - +
48S VAL* 3.5 29.8 - - + -
49S LEU 5.8 0.4 - - - +
54S ILE* 4.1 19.5 - - + +
72S VAL 4.2 2.5 - - - -
73S LYS* 1.3 75.0 - - - +
75S ARG* 1.3 63.6 + - - +
76S ALA* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P ASN* 3.8 10.1 + - - -
40P HIS* 5.4 0.7 - - - +
45P GLU* 4.3 11.1 + - - -
48P ILE* 5.6 5.3 - - - +
4S ILE* 3.1 39.1 + - + +
5S LYS 3.7 7.0 - - - +
6S ASP* 2.9 42.6 + - - +
7S LEU 4.5 0.4 - - - +
48S VAL* 3.8 5.7 - - - +
49S LEU* 3.0 40.5 + - + +
50S ASP* 5.2 10.5 - - + -
74S TYR* 1.3 77.4 - - - +
76S ALA* 1.3 68.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S ILE* 3.1 28.8 - - - +
5S LYS 3.1 14.3 + - - -
7S LEU* 4.7 13.0 - - + +
45S ILE* 5.0 7.4 - - + -
47S CYS 3.1 16.6 - - - +
48S VAL* 3.8 8.7 - - + -
49S LEU* 4.1 3.4 - - - +
74S TYR* 4.6 13.2 - - + -
75S ARG* 1.3 79.8 - - - +
77S VAL* 1.3 66.2 + - - +
78S VAL* 3.8 3.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50P LEU* 4.5 6.5 - - + -
55P ALA* 5.5 2.0 - - + +
58P VAL* 3.7 16.4 - - + -
59P ILE* 4.2 19.5 - - + +
2S PHE* 4.6 16.8 - - + -
3S PHE 3.5 5.2 - - - +
4S ILE* 3.8 10.1 - - + -
45S ILE 4.0 0.2 - - - -
46S LEU* 3.0 38.1 + - + +
47S CYS* 2.8 18.8 + - + +
49S LEU* 3.7 27.6 - - + -
76S ALA* 1.3 72.0 - - - +
78S VAL* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P PHE* 4.8 2.9 - - + -
2S PHE* 3.4 11.0 - - - -
3S PHE* 2.8 55.1 + - + +
5S LYS* 3.8 28.5 - - + +
7S LEU* 4.9 6.7 - - + -
42S PHE* 3.7 23.1 - - + +
44S TYR 3.1 15.9 - - - +
45S ILE* 3.5 30.1 - - + -
76S ALA* 4.5 2.2 - - + +
77S VAL* 1.3 76.0 - - - +
79S PHE* 1.3 60.0 + - - +
80S LYS 4.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1S MET* 3.1 38.6 - - + -
2S PHE* 3.9 25.4 - + + -
43S GLY* 4.0 0.2 - - - -
44S TYR* 2.8 35.0 + + + +
46S LEU* 3.9 18.4 - - + -
78S VAL* 1.3 76.5 - - - +
80S LYS* 1.3 57.0 + - - +
81S PRO* 3.5 10.1 - - + +
85S GLU* 5.8 0.4 - - - -
103S VAL* 3.4 28.5 - - + -
104S GLY* 4.8 1.3 - - - -
105S PRO* 3.2 32.1 - - + -
106S MET* 3.5 34.1 - - + -
----------------------------------------------------------
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