Contacts of the helix formed by residues 38 - 52 (chain C) in PDB entry 1H48
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 ASP 38 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 3.3 22.8 - - - +
20C ILE* 3.4 2.4 - - - -
21C GLY 2.8 19.9 + - - -
22C GLY* 2.7 28.4 + - - -
36C ASP* 3.1 18.8 + - - +
37C GLY* 1.3 73.8 - - - +
39C VAL* 1.3 60.6 + - - +
40C ALA 3.4 3.5 + - - -
41C LEU* 3.2 24.3 + - - +
42C HIS* 3.0 28.5 + - - -
73C SER* 3.6 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASP* 3.5 35.9 - - - +
9C VAL* 3.6 5.6 - - - +
10C HIS* 3.7 11.0 - - + +
19C ILE 4.5 0.4 + - - -
20C ILE* 3.7 24.9 - - + -
31C LEU* 3.9 9.4 - - + -
37C GLY 2.9 10.5 + - - +
38C ASP* 1.3 72.0 + - - +
40C ALA* 1.3 61.8 + - - +
42C HIS* 3.7 1.7 + - - +
43C ALA* 3.1 24.1 + - - +
146C ILE* 3.5 36.1 - - + +
148C CYS* 3.6 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 4.1 14.2 - - + +
21C GLY* 3.8 16.8 - - - +
38C ASP* 3.2 9.0 + - - +
39C VAL* 1.3 82.0 - - - +
41C LEU* 1.3 59.3 + - + +
43C ALA* 3.3 3.5 + - - +
44C LEU* 2.9 28.3 + - - +
96C VAL* 4.5 8.0 - - + +
98C ILE* 4.4 7.6 - - + -
112C MET* 5.6 0.7 - - - -
116C ILE* 6.2 1.8 - - + -
129C VAL* 6.2 0.4 - - + -
148C CYS* 3.5 24.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY* 3.9 12.3 - - - -
22C GLY 3.9 4.9 - - - +
38C ASP* 3.2 32.2 + - - +
40C ALA* 1.3 74.3 - - + +
42C HIS* 1.3 56.9 + - - +
44C LEU* 3.6 5.9 - - + +
45C THR* 2.5 40.6 + - - +
73C SER* 4.1 12.8 - - - +
74C ARG* 3.4 44.2 - - + +
77C LEU* 4.3 15.6 - - + +
115C PHE* 6.4 0.2 - - + -
116C ILE* 3.8 32.1 - - + -
119C ASP* 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASP* 3.1 17.7 + - - +
10C HIS* 3.3 5.3 + - - -
35C SER* 3.3 6.4 + - - -
37C GLY 4.6 0.2 - - - -
38C ASP 3.0 24.1 + - - +
39C VAL 3.8 0.9 - - - +
41C LEU* 1.3 77.0 - - - +
43C ALA* 1.3 57.7 + - - +
45C THR* 3.3 7.0 + - - -
46C ASP* 2.9 34.2 + - - +
57C ILE* 4.3 11.0 - - + +
73C SER* 2.8 30.0 + - - -
76C LEU* 4.8 4.2 - - + +
902C CDI 2.9 52.6 + - + +
903C ZN 2.2 27.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLY* 3.4 12.8 - - - +
7C PHE 4.0 12.8 - - - +
8C ASP* 4.0 11.4 - - - +
39C VAL 3.1 17.3 + - - +
40C ALA 3.8 3.4 - - - +
42C HIS* 1.3 77.8 - - - +
44C LEU* 1.3 62.7 + - - +
46C ASP* 3.4 1.2 + - - -
47C ALA 3.0 17.2 + - - -
148C CYS* 3.4 35.9 - - + +
149C GLU* 4.3 3.6 - - - +
150C ALA* 3.7 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA 2.9 17.5 + - - +
41C LEU* 3.6 12.6 - - + +
43C ALA* 1.3 76.9 - - - +
45C THR* 1.3 62.4 + - - +
47C ALA* 3.1 7.9 + - + +
48C LEU* 3.0 32.9 + - + +
77C LEU* 4.3 12.3 - - + -
94C VAL* 3.8 35.2 - - + -
96C VAL* 4.2 14.8 - - + -
116C ILE* 3.7 43.7 - - + -
120C LEU* 4.7 2.7 - - + -
150C ALA* 3.7 14.5 - - + +
151C VAL 5.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 2.5 29.8 + - - +
42C HIS* 3.6 6.7 - - - -
44C LEU* 1.3 71.5 - - - +
46C ASP* 1.3 59.5 + - - +
48C LEU* 3.2 4.7 + - - +
49C LEU* 2.9 36.3 + - + +
57C ILE* 3.3 28.0 - - + -
61C PHE* 5.0 0.4 - - + -
73C SER 5.0 1.0 + - - -
76C LEU* 4.4 8.3 - - + +
77C LEU* 3.6 27.5 + - + +
80C ALA* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A THR* 6.2 0.3 - - - +
130A LYS* 3.4 27.3 - - - +
131A ALA 5.0 1.7 - - - +
132A THR* 5.0 8.3 - - - -
6C GLY* 3.9 7.2 - - - -
7C PHE 4.5 10.4 + - - +
8C ASP* 6.0 0.3 - - - +
42C HIS 2.9 14.4 + - - +
43C ALA* 3.7 5.8 - - - +
44C LEU 3.3 0.2 - - - -
45C THR* 1.3 76.2 - - - +
47C ALA* 1.3 52.9 + - - +
49C LEU* 3.9 3.1 - - - +
50C GLY* 2.8 29.3 + - - -
56C ASP* 3.2 17.6 - - - +
57C ILE* 2.8 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLY* 3.2 12.7 - - - +
5C HIS 3.7 15.3 - - - +
6C GLY* 3.7 2.8 - - - +
43C ALA 3.0 11.0 + - - +
44C LEU* 3.1 9.8 + - + +
46C ASP* 1.3 76.2 - - - +
48C LEU* 1.3 58.0 + - - +
51C ALA* 3.1 23.7 + - - +
150C ALA* 3.6 33.7 - - + +
151C VAL 4.6 0.2 - - - +
152C ALA* 3.9 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 3.0 30.2 + - + +
45C THR* 3.6 6.1 - - + +
47C ALA* 1.3 74.9 - - - +
49C LEU* 1.3 63.9 + - - +
51C ALA* 3.3 5.5 + - - +
52C ALA* 3.1 18.4 + - - +
77C LEU* 3.7 28.7 - - + -
80C ALA* 6.1 0.7 - - + -
81C TRP* 4.2 10.1 - - + -
84C ILE* 3.6 22.7 - - + +
91C LEU* 3.9 18.4 - - + -
94C VAL* 4.1 3.4 - - + -
120C LEU* 4.0 16.4 - - + -
152C ALA* 3.9 13.2 - - + -
154C LEU* 3.8 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C THR* 2.9 31.7 + - + +
46C ASP* 3.9 4.0 - - - +
48C LEU* 1.3 73.7 - - - +
50C GLY* 1.3 60.3 + - - +
52C ALA* 3.3 2.0 + - - +
53C ALA 3.0 7.4 + - - -
54C LEU* 2.8 51.1 + - + -
55C GLY 4.0 12.1 - - - +
56C ASP* 3.5 33.0 - - - +
57C ILE* 3.6 7.0 - - + +
60C LEU* 3.8 28.0 - - + -
80C ALA* 3.9 17.3 - - + +
84C ILE* 3.7 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASN* 4.4 3.3 + - - -
95A ASP* 3.4 25.9 - - - +
128A ASN* 3.4 34.7 - - - +
130A LYS* 4.5 0.2 - - - -
3C ILE 4.3 0.3 - - - +
46C ASP 2.8 19.0 + - - -
48C LEU 3.3 0.2 - - - -
49C LEU* 1.3 73.8 - - - +
51C ALA* 1.3 60.4 + - - +
53C ALA* 3.1 9.7 + - - +
55C GLY 4.1 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASN* 4.0 0.6 + - - +
2C ARG* 2.6 44.5 + - - +
3C ILE 3.3 32.3 - - - -
4C GLY* 3.6 2.2 - - - +
47C ALA 3.1 15.4 + - - +
48C LEU* 3.3 2.2 + - - +
50C GLY* 1.3 76.2 - - - +
52C ALA* 1.3 53.2 + - - +
53C ALA 3.2 0.7 + - - -
152C ALA* 4.5 3.4 - - + +
154C LEU* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ARG* 4.5 2.5 - - - -
48C LEU 3.1 15.6 + - - +
49C LEU 3.9 2.9 - - - +
50C GLY 3.2 0.2 - - - -
51C ALA* 1.3 76.4 - - - +
53C ALA* 1.3 62.9 + - - +
54C LEU* 3.3 9.5 + - + +
84C ILE* 3.7 23.6 - - + -
87C LYS* 2.9 28.5 + - + -
89C TYR* 3.9 25.4 + - + -
154C LEU* 3.9 6.7 - - + -
----------------------------------------------------------
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