Contacts of the helix formed by residues 102 - 112 (chain D) in PDB entry 4HXD
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 SER 102 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ARG* 5.0 1.5 + - - -
71C LEU 4.7 1.3 + - - -
72C ARG* 4.3 0.9 - - - -
73C LEU* 2.9 40.4 + - - -
78D GLU* 2.4 40.1 + - - +
101D GLY* 1.3 68.7 - - - -
103D LEU* 1.3 64.1 + - - +
105D ALA 3.5 0.3 + - - -
106D SER* 3.2 18.0 + - - -
118D LEU* 3.8 14.2 - - - +
131D ILE* 4.9 4.0 - - - -
133D PHE* 3.3 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ARG* 4.3 18.6 - - - +
73D TYR* 4.4 2.5 - - + +
76D GLU* 4.1 16.4 - - + +
78D GLU* 3.2 24.6 + - + +
79D ALA* 3.5 43.7 - - + +
82D THR* 6.2 0.4 - - + -
89D TYR* 3.6 33.0 - - + -
102D SER* 1.3 80.2 + - - +
104D GLU* 1.3 70.9 + - - +
106D SER* 3.4 5.6 + - - -
107D MET* 3.3 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ARG* 5.4 3.3 - - - +
41D PHE* 3.8 15.9 - - + -
42D TYR* 3.1 26.2 - - + +
65D LEU* 3.8 15.9 - - + -
89D TYR* 2.6 38.3 + - - +
93D ALA* 4.8 2.8 - - - +
99D TRP 5.0 2.2 - - - +
100D GLY* 3.5 6.1 - - - -
101D GLY* 2.8 31.6 + - - +
102D SER 3.3 0.2 - - - -
103D LEU* 1.3 84.1 + - - +
105D ALA* 1.3 61.2 - - - +
107D MET* 3.4 2.7 + - - +
108D LEU* 3.0 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PHE* 4.0 9.8 - - + -
101D GLY 2.9 17.5 + - - +
102D SER 3.7 0.2 - - - +
104D GLU* 1.3 76.6 - - - +
106D SER* 1.3 53.1 + - - +
108D LEU* 4.7 0.9 - - - -
109D SER* 2.8 37.1 + - - -
116D ILE* 3.4 27.7 - - + +
118D LEU* 4.3 6.3 - - + -
133D PHE* 3.6 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLN* 3.5 12.6 + - - +
76D GLU* 2.6 26.9 + - - -
78D GLU* 5.5 1.3 - - - -
102D SER 3.2 10.9 + - - -
103D LEU* 3.6 5.6 - - - -
105D ALA* 1.3 80.0 - - - +
107D MET* 1.3 60.2 + - - +
109D SER* 3.5 7.2 - - - -
110D LYS* 3.0 34.8 + - - +
133D PHE* 3.6 30.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LEU* 3.7 16.6 - - + -
68D ALA* 3.7 14.3 - - + +
69D ALA* 3.8 26.2 - - + -
72D TYR* 4.2 9.4 - - + -
73D TYR* 4.1 24.7 - - + -
76D GLU* 3.1 25.1 - - + +
89D TYR* 3.4 37.9 - - + +
103D LEU* 3.3 22.8 + - + +
104D GLU* 4.0 2.0 - - - +
105D ALA 3.3 0.2 - - - -
106D SER* 1.3 73.1 - - - +
108D LEU* 1.3 61.5 - - - +
110D LYS* 3.4 4.6 + - - +
111D HIS* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D PHE* 4.5 6.7 - - + -
42D TYR* 4.6 2.9 - - + -
45D ILE* 4.0 18.2 - - + -
61D VAL* 3.8 42.2 - - + +
64D HIS* 3.8 14.8 - - + +
65D LEU* 3.8 30.3 - - + +
68D ALA* 4.8 1.3 - - + -
104D GLU 3.0 24.0 + - - +
105D ALA 4.0 2.7 - - - +
107D MET* 1.3 73.4 - - - +
109D SER* 1.3 60.8 + - - +
111D HIS* 4.4 3.1 - - - +
112D LEU* 2.9 46.6 + - + +
116D ILE* 4.1 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ALA 2.8 19.5 + - - -
106D SER 3.5 8.1 - - - -
108D LEU* 1.3 76.5 - - - +
110D LYS* 1.3 62.5 + - - +
113D GLN* 3.3 2.8 + - - -
114D THR 3.0 44.3 + - - -
116D ILE* 3.7 5.8 - - - +
133D PHE* 3.3 31.6 + - - -
134D GLY* 3.8 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLU* 3.7 10.4 - - - +
14D ASP* 6.1 5.8 - - - -
15D GLU* 5.9 8.1 - - - -
16D GLN* 5.4 0.6 - - - +
72D TYR* 3.6 45.9 + - + +
75D THR* 6.1 0.4 - - - -
76D GLU* 2.5 35.7 + - - -
77D PRO* 5.8 1.6 - - - +
106D SER* 3.0 28.6 + - - +
107D MET 3.4 4.0 + - - +
108D LEU 3.2 0.6 - - - -
109D SER* 1.3 77.3 - - - +
111D HIS* 1.3 68.5 + - - +
113D GLN* 3.0 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLU* 3.3 28.6 - - - +
17B TYR* 5.3 2.9 + - - -
135B PRO* 3.3 32.8 - - + +
64D HIS* 2.7 42.8 - + + +
67D LEU* 4.1 17.8 - - + +
68D ALA* 3.5 34.5 - - + -
71D VAL* 6.0 2.7 - - + -
72D TYR* 3.8 5.0 - + + -
107D MET 3.0 15.6 + - - +
108D LEU* 4.0 3.1 - - - +
110D LYS* 1.3 79.9 - - - +
112D LEU* 1.3 71.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLN* 5.8 0.7 - - - +
135B PRO* 4.3 11.3 - - + +
45D ILE* 5.3 10.3 - - + -
49D PHE* 3.9 38.6 - - + -
61D VAL* 5.4 2.7 - - + -
64D HIS* 3.4 41.1 - - + +
108D LEU* 2.9 43.1 + - + +
111D HIS* 1.3 79.6 - - + +
113D GLN* 1.3 70.4 + - - +
114D THR* 3.1 18.1 + - - +
116D ILE* 5.2 5.6 - - + -
142D LEU* 5.6 1.8 - - + -
----------------------------------------------------------
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