Contacts of the helix formed by residues 102 - 112 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 5.5 3.3 - - - -
71A LEU 5.4 0.9 - - - -
72A ARG* 4.4 0.7 - - - -
73A LEU* 2.8 39.4 + - - -
78B GLU* 2.6 37.0 + - - +
101B GLY* 1.3 68.9 - - - -
103B LEU* 1.3 58.9 + - - +
105B ALA* 3.5 1.3 - - - +
106B SER* 2.9 31.4 + - - -
118B LEU* 3.8 12.8 - - - +
131B ILE* 5.0 4.3 - - - -
133B PHE* 3.5 17.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 5.5 7.9 - - - +
73B TYR* 4.7 2.7 - - + +
76B GLU* 4.2 13.5 - - + +
78B GLU* 2.8 30.5 + - + +
79B ALA* 3.8 40.8 - - + +
82B THR* 6.0 3.4 - - + -
89B TYR* 3.6 29.6 - - + -
101B GLY 3.4 0.6 - - - -
102B SER* 1.3 77.4 + - - +
104B GLU* 1.3 70.4 + - - +
106B SER* 3.4 4.7 + - - -
107B MET* 3.2 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 4.7 9.6 + - - -
41B PHE* 3.6 19.7 - - + -
42B TYR* 3.4 19.7 + - + +
65B LEU* 3.8 10.5 - - + -
89B TYR* 2.9 39.9 + - - +
93B ALA* 4.9 2.3 - - - +
99B TRP 5.1 0.6 - - - +
100B GLY* 3.4 9.0 - - - -
101B GLY 2.8 25.0 + - - -
103B LEU* 1.3 81.7 - - - +
105B ALA* 1.3 65.8 + - - +
107B MET* 4.5 6.5 - - - -
108B LEU* 3.0 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.8 8.0 - - + -
101B GLY 2.8 18.0 + - - +
102B SER* 3.2 6.9 + - - +
104B GLU* 1.3 78.7 - - - +
106B SER* 1.3 62.9 + - - +
108B LEU* 4.8 0.2 - - - -
109B SER* 3.0 22.7 + - - -
116B ILE* 3.4 20.5 - - + +
118B LEU* 4.1 17.0 - - + -
133B PHE* 3.5 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLN* 3.6 15.3 + - - +
76B GLU* 2.7 29.5 + - - -
78B GLU* 5.4 1.3 - - - -
102B SER 2.9 16.7 + - - -
103B LEU* 3.6 3.6 - - - -
105B ALA* 1.3 76.1 - - - +
107B MET* 1.3 64.7 + - - +
109B SER* 2.9 21.9 + - - -
110B LYS* 3.4 14.7 + - - +
133B PHE* 3.6 26.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 3.9 9.4 - - + -
68B ALA* 4.0 14.6 - - + +
69B ALA* 3.8 26.9 - - - -
72B TYR* 4.3 6.5 - - + -
73B TYR* 4.1 20.0 - - + -
76B GLU* 3.6 24.2 - - + +
89B TYR* 3.1 41.7 - - + +
103B LEU* 3.2 32.4 + - + +
104B GLU* 4.1 3.6 - - - +
106B SER* 1.3 78.2 + - - +
108B LEU* 1.3 62.5 + - - +
110B LYS* 3.3 11.5 + - - +
111B HIS* 3.2 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 4.5 15.7 - - + -
42B TYR* 4.7 4.5 - - + -
45B ILE* 4.6 7.6 - - + -
61B VAL* 3.8 29.2 - - + +
64B HIS* 3.9 13.0 - - + +
65B LEU* 3.6 38.1 - - + +
68B ALA* 4.6 2.5 - - + -
104B GLU* 3.0 31.6 + - + +
105B ALA* 5.1 0.4 - - - -
107B MET* 1.3 74.8 - - - +
109B SER* 1.3 60.2 + - - +
111B HIS* 4.2 2.9 - - + -
112B LEU* 2.8 53.8 + - + +
116B ILE* 4.0 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ALA 3.0 15.9 + - - -
106B SER* 2.9 14.1 + - - -
108B LEU* 1.3 76.7 - - - +
110B LYS* 1.3 60.1 + - - +
112B LEU* 5.1 0.4 - - - -
113B GLN* 3.3 15.2 + - - -
114B THR 2.9 31.3 - - - +
116B ILE* 3.6 10.7 - - - +
133B PHE* 3.5 27.7 + - - +
134B GLY* 5.3 0.2 - - - -
113D GLN* 3.2 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP* 5.3 7.9 + - - +
16B GLN* 5.7 0.8 - - - +
72B TYR* 3.7 48.8 + - + +
75B THR* 4.6 11.5 + - - -
76B GLU* 2.7 37.0 + - - +
77B PRO* 5.1 3.2 - - - +
106B SER* 3.8 14.4 + - - +
107B MET 3.3 7.3 + - - +
108B LEU 3.1 0.2 - - - -
109B SER* 1.3 80.5 + - - +
111B HIS* 1.3 63.4 + - - +
113B GLN* 3.6 17.5 + - - +
113D GLN* 3.4 54.4 - - + +
137D ARG* 5.1 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B HIS* 3.2 52.1 + + - +
67B LEU* 3.6 19.0 - - + +
68B ALA* 3.5 38.8 - - + -
72B TYR* 4.6 1.8 - - + -
107B MET 3.2 2.3 + - - +
108B LEU* 3.0 8.4 + - - +
110B LYS* 1.3 81.1 - - - +
112B LEU* 1.3 63.8 + - + +
113B GLN* 3.2 8.5 + - - +
137D ARG* 2.9 42.2 + - - +
140D THR* 5.7 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 5.4 9.2 - - + -
49B PHE* 3.6 43.9 - - + -
61B VAL* 5.4 4.9 - - + -
64B HIS* 3.7 30.5 - - + +
108B LEU* 2.8 50.0 + - + +
109B SER* 5.1 0.7 - - - -
111B HIS* 1.3 78.0 - - - +
113B GLN* 1.3 71.1 + - - +
114B THR* 3.1 17.2 + - - +
116B ILE* 4.7 8.7 - - + -
142B LEU* 5.6 4.0 - - + -
----------------------------------------------------------
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