Contacts of the helix formed by residues 26 - 37 (chain B) in PDB entry 1HF0
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 THR 26 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 4.4 13.2 - - - +
20B ARG* 4.2 3.4 - - - +
24B GLY 5.5 0.7 - - - +
25B PHE* 1.3 77.8 - - - +
27B GLN* 1.3 66.3 + - - +
28B GLY* 3.1 6.0 + - - -
29B ASP* 2.6 51.6 + - - +
30B VAL* 2.9 12.5 + - - +
10N C 4.1 26.8 + - - +
11N C 3.3 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS* 5.5 1.4 - - - +
20B ARG* 2.7 36.1 - - - +
26B THR* 1.3 70.9 - - - +
28B GLY* 1.3 57.7 + - - +
30B VAL* 3.2 5.1 + - - +
31B GLY* 3.0 21.5 + - - -
44B GLN* 4.3 11.7 - - + +
47B ILE* 3.7 25.3 - - + +
48B SER* 2.8 37.3 + - - +
51B GLU* 3.1 13.5 + - - -
11N C 3.0 33.8 + - + +
12N T 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR* 3.0 6.7 + - - -
27B GLN* 1.3 78.8 - - - +
29B ASP* 1.3 59.2 + - - +
31B GLY* 3.0 2.6 + - - -
32B LEU* 2.9 34.4 + - - +
44B GLN* 3.9 23.5 - - - +
11N C 4.6 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 3.6 17.2 + - - -
24B GLY 4.4 2.4 - - - +
25B PHE* 3.1 34.5 - - + -
26B THR* 2.6 49.6 + - - +
28B GLY* 1.3 71.5 - - - -
30B VAL* 1.3 54.3 + - - +
32B LEU* 3.4 17.3 + - - +
33B ALA* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PHE* 4.2 4.7 - - + -
20B ARG* 4.2 17.0 - - + -
25B PHE* 4.4 3.8 - - + -
26B THR 2.9 12.6 + - - +
27B GLN 3.5 8.3 - - - +
29B ASP* 1.3 72.9 - - - +
31B GLY* 1.3 61.1 + - - +
33B ALA* 3.6 5.8 - - - +
34B MET* 2.8 48.0 + - + +
47B ILE* 3.3 29.6 - - + -
67B LEU* 4.0 11.4 - - + -
70B TRP* 3.2 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN 3.0 11.1 + - - -
28B GLY* 3.0 9.4 + - - -
30B VAL* 1.3 81.9 - - - +
32B LEU* 1.3 61.4 + - - +
34B MET* 3.2 5.6 + - - +
35B GLY* 3.1 16.8 + - - -
42B PHE 3.1 28.6 + - - +
44B GLN 5.1 2.7 - - - -
47B ILE* 4.6 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.3 26.5 - - + -
28B GLY 2.9 17.2 + - - +
29B ASP* 3.7 19.7 - - - +
31B GLY* 1.3 72.3 - - - +
33B ALA* 1.3 67.9 + - - +
35B GLY* 3.1 13.6 + - - -
36B LYS* 3.6 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE* 4.9 9.4 - - + -
29B ASP 2.9 18.0 + - - +
30B VAL* 3.6 6.3 - - - +
32B LEU* 1.3 74.8 - - - +
34B MET* 1.3 54.6 + - - +
36B LYS* 2.7 34.7 + - - +
37B LEU* 3.3 13.6 + - + +
70B TRP* 4.0 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 2.8 39.9 + - + +
31B GLY* 3.5 4.9 - - - +
33B ALA* 1.3 72.0 - - - +
35B GLY* 1.3 60.6 + - - +
36B LYS 3.1 1.4 + - - -
37B LEU* 4.3 2.9 - - - -
38B TYR* 3.6 15.1 + - + +
39B GLY 3.4 16.5 + - - -
40B ASN* 3.6 7.9 + - - +
42B PHE* 3.8 39.5 - - + -
47B ILE* 4.6 6.5 - - + -
63B LEU 6.0 0.2 - - - +
66B LEU* 4.2 17.3 - - + +
67B LEU* 3.8 33.7 - - + +
70B TRP* 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLY 3.1 8.6 + - - -
32B LEU* 3.1 9.2 + - - -
33B ALA 2.8 4.6 + - - -
34B MET* 1.3 74.0 - - - +
36B LYS* 1.3 61.3 + - - +
39B GLY* 3.5 14.0 - - - -
40B ASN 3.4 20.2 - - - +
41B ASP* 5.2 2.0 - - - -
42B PHE 5.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.8 20.8 - - - +
33B ALA* 2.7 15.5 + - - +
35B GLY* 1.3 75.8 - - - +
37B LEU* 1.3 74.5 + - - +
39B GLY* 2.7 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 3.3 11.8 + - + +
34B MET* 4.8 2.5 - - - +
36B LYS* 1.3 85.2 - - - +
38B TYR* 1.3 56.4 + - + +
39B GLY* 2.5 8.3 + - - -
70B TRP* 5.1 15.0 - - + -
73B ASP* 6.3 2.9 - - - -
----------------------------------------------------------
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