Contacts of the helix formed by residues 100 - 112 (chain B) in PDB entry 5M73
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 100 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 4.3 10.7 - - - +
98B PHE 3.3 2.0 + - - -
99B PRO* 1.3 83.7 - - - +
101B ARG* 1.3 65.4 + - - +
102B LYS* 3.8 8.5 + - - +
103B SER* 2.4 40.6 + - - -
104B VAL* 3.4 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A G 3.1 62.2 + - - -
148A G 3.2 30.1 + - - -
149A A 3.1 34.0 + - - -
16B ILE* 3.9 28.3 - - + +
17B CYS 5.7 2.9 - - - +
18B ILE* 5.4 1.0 - - + +
86B LEU* 4.4 5.0 - - + +
100B SER* 1.3 74.6 - - - +
102B LYS* 1.3 65.5 + - - +
104B VAL* 3.0 20.0 + - - +
105B MET* 3.1 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A C 4.5 25.6 - - - +
34B ARG* 3.3 27.5 + - - +
35B ILE* 4.4 8.2 - - + +
100B SER* 3.2 8.4 + - - +
101B ARG* 1.3 77.3 - - - +
103B SER* 1.3 57.9 + - - +
105B MET* 2.8 39.7 + - - +
106B LEU* 2.9 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLN 4.8 3.1 - - - -
98B PHE* 3.7 22.9 - - - +
99B PRO* 4.5 7.0 - - - -
100B SER* 2.4 39.0 + - - -
102B LYS* 1.3 77.8 - - - +
104B VAL* 1.3 62.4 + - - +
106B LEU* 3.4 13.6 + - - +
107B TYR* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 5.1 2.5 - - + -
18B ILE* 3.5 27.4 - - + -
53B CYS* 4.3 19.5 - - - -
58B LEU* 4.8 4.9 - - + -
84B VAL* 4.7 11.7 - - + -
86B LEU* 4.3 18.8 - - + -
98B PHE* 4.1 26.7 - - + -
100B SER 3.7 13.5 - - - +
101B ARG* 3.0 9.9 + - - +
103B SER* 1.3 77.5 + - - +
105B MET* 1.3 68.3 + - - +
107B TYR* 3.0 7.9 + - + +
108B ALA* 2.9 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B CYS 5.4 2.2 - - - +
18B ILE* 4.2 23.8 - - + -
22B TYR* 3.9 35.2 - - + -
23B LEU* 3.6 24.4 - - + +
34B ARG* 4.4 18.6 - - + -
35B ILE* 4.3 8.1 - - + -
101B ARG* 3.1 28.4 + - + +
102B LYS* 2.8 29.5 + - - +
104B VAL* 1.3 74.6 - - - +
106B LEU* 1.3 65.2 + - - +
108B ALA* 2.9 18.3 + - - +
109B ALA* 3.0 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 4.0 22.0 - - + -
36B PRO* 5.1 2.2 - - + -
39B LYS* 3.9 40.2 - - + +
102B LYS* 2.9 32.7 + - + +
103B SER* 3.8 12.3 - - - +
105B MET* 1.3 76.7 - - - +
107B TYR* 1.3 63.9 + - - +
109B ALA* 3.1 8.4 + - - +
110B GLU* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.6 11.9 - - + -
53B CYS* 5.5 4.7 - - - -
56B VAL* 3.4 40.7 - - + +
98B PHE* 4.0 29.4 - + + -
103B SER 3.0 17.3 + - - +
104B VAL* 3.0 5.8 + - + +
106B LEU* 1.3 76.5 - - - +
108B ALA* 1.3 67.5 + - - +
110B GLU* 2.9 24.7 + - - +
111B MET* 2.9 59.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 5.8 1.3 - - + -
23B LEU* 3.6 18.8 - - + -
49B ILE* 4.5 13.0 - - + -
52B VAL* 4.2 20.4 - - + -
53B CYS* 4.9 4.2 - - - -
104B VAL* 2.9 12.7 + - + +
105B MET* 2.9 10.1 + - - +
107B TYR* 1.3 77.1 - - - +
109B ALA* 1.3 65.5 + - - +
111B MET* 3.1 0.5 + - - +
112B ILE* 2.9 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.2 5.8 - - + +
35B ILE* 4.4 11.2 - - + -
39B LYS* 3.5 29.6 - - + +
40B ALA* 4.3 8.3 - - - -
41B VAL* 3.4 17.3 - - + +
105B MET 3.0 11.5 + - - +
106B LEU* 3.5 9.4 - - - +
108B ALA* 1.3 75.8 - - - +
110B GLU* 1.3 60.9 + - - +
112B ILE* 4.7 4.9 - - - -
113B PRO* 3.3 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU 2.9 12.6 + - - +
107B TYR* 2.9 19.1 + - - +
109B ALA* 1.3 80.2 - - - +
111B MET* 1.3 81.6 + - + +
113B PRO* 3.5 7.6 - - - +
114B LYS* 5.0 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.2 17.9 - - + -
107B TYR* 2.9 66.3 + - + +
108B ALA 4.2 0.7 - - - +
110B GLU* 1.3 97.4 - - + +
112B ILE* 1.3 67.9 + - - +
113B PRO 3.2 0.2 - - - -
114B LYS* 2.8 43.6 + - + +
115B LEU* 4.1 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.5 2.5 - - + -
41B VAL* 4.3 16.6 - - + -
42B GLU 5.9 0.9 - - - +
44B PRO* 3.6 25.1 - - + -
48B GLU* 3.9 33.8 - - + +
49B ILE* 4.0 20.6 - - + -
52B VAL* 4.4 21.1 - - + +
108B ALA* 2.9 32.3 + - + +
109B ALA 4.4 1.3 - - - +
111B MET* 1.3 76.3 - - - +
113B PRO* 1.3 69.7 - - + +
114B LYS 3.0 1.4 + - - -
115B LEU* 3.3 18.0 + - - +
116B LYS 4.9 0.3 + - - -
117B THR* 4.3 3.9 + - - +
----------------------------------------------------------
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