Contacts of the helix formed by residues 36 - 51 (chain A) in PDB entry 4HFG
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 HIS 36 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A HIS* 2.8 27.6 + - + +
35A LYS* 1.4 77.2 - - + +
37A ALA* 1.3 58.8 + - - +
38A GLY 3.4 2.2 - - - -
39A PRO* 3.3 15.4 - - + +
40A ILE* 2.9 35.2 + - + +
205A UNX 3.3 27.0 - - - -
4B PHE* 3.4 39.1 - + + -
205B UNX 3.8 13.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG 3.0 18.1 + - - +
35A LYS 3.4 2.2 + - - -
36A HIS* 1.3 78.1 - - - +
38A GLY* 1.3 63.4 + - - +
40A ILE* 3.6 1.1 - - - +
41A VAL* 3.0 28.6 + - - +
76A GLU* 3.8 20.9 - - + +
77A PHE* 3.8 29.4 - - + -
80A GLU* 3.9 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 1.3 77.0 - - - +
39A PRO* 1.3 70.3 - - - +
41A VAL* 3.1 5.0 + - - +
42A SER* 2.9 23.0 + - - -
80A GLU* 3.6 28.4 - - - +
209A UNX 3.4 11.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS 5.6 0.7 - - - +
36A HIS* 3.3 20.9 - - + +
38A GLY* 1.3 88.2 - - - +
40A ILE* 1.3 60.3 + - - +
42A SER* 3.3 5.1 + - - -
43A VAL* 3.0 30.7 + - - +
209A UNX 3.8 14.1 - - - -
4B PHE* 4.8 11.9 - - + -
6B GLU* 3.8 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.8 35.0 - - + +
33A HIS* 3.5 24.0 - - + +
36A HIS* 2.9 21.9 + - + +
37A ALA 3.6 4.0 - - - +
38A GLY 3.3 0.2 - - - -
39A PRO* 1.3 76.2 - - - +
41A VAL* 1.3 59.9 + - + +
43A VAL* 3.7 1.7 - - - +
44A TRP* 2.8 31.8 + - + +
77A PHE* 3.8 31.4 - - + -
81A PHE* 5.4 3.4 - - + -
4B PHE* 3.3 32.5 - - + -
9B LEU* 3.8 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA 3.0 21.7 + - - +
38A GLY* 3.6 3.4 - - - +
40A ILE* 1.3 74.4 - - - +
42A SER* 1.3 59.4 + - - +
44A TRP* 3.6 7.2 - - - +
45A HIS* 3.0 29.5 + - - +
77A PHE* 4.4 4.7 - - + -
80A GLU* 3.6 34.1 - - + +
81A PHE* 3.8 36.8 - - + -
84A VAL* 3.6 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY 2.9 16.0 + - - -
39A PRO* 3.7 8.7 - - - -
40A ILE 3.3 0.2 - - - -
41A VAL* 1.3 78.7 - - - +
43A VAL* 1.3 61.6 + - - +
45A HIS* 3.4 5.2 + - - +
46A ARG* 3.2 31.4 + - - +
84A VAL* 5.9 1.8 - - - -
209A UNX 4.4 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO 3.0 21.6 + - - +
40A ILE 3.7 3.4 - - - +
42A SER* 1.3 72.2 - - - +
44A TRP* 1.3 67.1 + - - +
46A ARG* 3.4 18.0 + - - +
47A GLU* 2.9 38.6 + - + +
4B PHE* 5.6 0.2 - - + -
6B GLU* 3.7 39.9 - - + +
9B LEU* 3.7 27.4 - - + -
10B GLU* 4.0 14.6 - - + -
13B LEU* 4.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 2.8 25.3 + - + +
41A VAL* 3.6 8.7 - - - +
43A VAL* 1.3 71.7 - - - +
45A HIS* 1.3 82.3 + + + +
48A LEU* 2.9 37.1 + - + +
59A PHE* 2.8 59.3 + + + +
60A LEU* 3.6 17.7 - - + -
62A LEU* 4.0 20.5 - - + +
63A ALA* 3.9 7.6 - - + +
81A PHE* 3.7 26.1 - + + -
84A VAL* 3.7 23.6 - - + -
85A LEU* 4.3 7.0 - - + -
88A ALA* 3.5 30.3 - - + -
9B LEU* 5.4 0.7 - - + -
13B LEU* 4.1 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL 3.0 18.1 + - - +
42A SER* 3.6 6.9 - - - +
43A VAL 3.1 0.2 - - - -
44A TRP* 1.3 94.0 - + + +
46A ARG* 1.3 61.7 + - - +
48A LEU* 3.4 22.3 - - + +
49A ARG* 3.5 15.8 + - + +
83A SER 5.8 0.4 - - - -
84A VAL* 3.5 36.6 + - + +
87A ASP* 2.6 37.1 + - + +
88A ALA 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER* 3.2 18.4 + - - +
43A VAL* 3.8 30.4 - - - +
45A HIS* 1.3 78.4 - - - +
47A GLU* 1.3 82.6 + - - +
49A ARG* 3.2 16.6 + - - +
50A LYS* 3.2 22.6 + - + +
6B GLU* 4.7 6.3 + - - -
10B GLU* 2.9 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 2.9 35.5 + - + +
46A ARG* 1.3 95.4 + - - +
48A LEU* 1.3 66.3 + - - +
50A LYS* 3.1 36.1 + - - +
51A ALA* 2.9 24.8 + - - +
59A PHE* 3.6 17.8 - - + -
10B GLU* 3.8 24.6 - - + +
13B LEU* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TRP* 2.9 26.6 + - + +
45A HIS* 3.4 17.5 - - + +
47A GLU* 1.3 76.8 - - - +
49A ARG* 1.3 63.3 + - + +
51A ALA* 3.2 7.8 + - - +
56A LYS* 3.1 48.6 + - + +
59A PHE* 3.3 26.1 - - + -
87A ASP* 5.7 0.2 - - - +
88A ALA* 3.8 37.7 - - + +
91A HIS* 3.9 14.4 - - + -
92A VAL* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A HIS* 3.5 17.6 + - + +
46A ARG* 3.2 10.8 + - - +
48A LEU* 1.3 82.1 - - + +
50A LYS* 1.3 62.0 + - + +
56A LYS* 3.2 11.1 + - - -
87A ASP* 2.6 41.3 + - - +
91A HIS* 3.3 44.0 + - + +
94A ARG* 4.3 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 3.2 23.7 + - + +
47A GLU* 3.1 42.9 + - - +
49A ARG* 1.3 78.8 - - + +
51A ALA* 1.3 62.1 + - - +
52A LYS* 3.7 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU 2.9 15.9 + - - +
48A LEU 3.2 9.6 + - - +
50A LYS* 1.3 78.9 - - - +
52A LYS* 1.3 69.1 + - - +
55A ARG* 4.3 7.6 - - + -
56A LYS* 2.7 29.9 + - + -
59A PHE* 3.6 28.5 - - + -
----------------------------------------------------------
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