Contacts of the helix formed by residues 102 - 117 (chain A) in PDB entry 3NT2
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 102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 4.3 5.2 + - - -
100A ALA* 3.1 1.3 - - - +
101A THR* 1.3 92.9 + - - +
103A ALA* 1.3 66.0 + - - +
104A GLU* 3.3 17.7 + - - +
105A GLY* 3.2 25.8 + - - -
106A CYS* 3.3 16.5 + - - -
108A ARG* 4.5 3.6 + - - -
309A ALA* 4.2 6.1 - - - -
313A ASP* 4.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR* 1.3 73.7 - - - +
104A GLU* 1.3 68.5 + - - +
106A CYS* 3.3 4.3 + - - +
107A MET* 3.0 24.6 + - - +
306A TYR* 3.6 12.6 - - + -
309A ALA* 4.0 11.7 - - - +
310A VAL* 4.0 28.0 - - + +
313A ASP* 3.9 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR* 3.4 19.1 - - - +
103A ALA* 1.3 84.4 + - - +
105A GLY* 1.3 61.2 + - - +
107A MET* 2.9 24.3 + - - +
108A ARG* 2.9 37.0 + - - +
313A ASP* 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 3.3 34.4 - - - -
100A ALA* 3.7 8.3 - - - -
102A THR* 3.2 13.3 + - - -
104A GLU* 1.3 80.0 - - - +
106A CYS* 1.3 59.8 + - - +
108A ARG* 3.7 7.2 + - - +
109A ILE* 3.3 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 4.2 11.4 - - + +
100A ALA* 3.9 23.6 - - - -
102A THR 3.3 6.8 + - - -
103A ALA 3.5 7.9 - - - +
104A GLU 3.1 0.6 - - - -
105A GLY* 1.3 75.2 - - - +
107A MET* 1.3 59.6 + - - +
109A ILE* 3.1 8.0 + - - +
110A VAL* 2.8 33.6 + - - +
305A GLY 3.6 14.4 - - - -
306A TYR* 3.6 22.0 - - + +
309A ALA* 3.6 27.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA 3.0 9.4 + - - +
104A GLU* 2.9 13.2 + - - +
106A CYS* 1.3 76.4 - - - +
108A ARG* 1.3 57.8 + - + +
110A VAL* 4.3 11.4 - - + -
111A GLU* 2.8 68.2 + - + +
303A TRP* 4.2 20.6 - - + -
306A TYR* 3.7 28.9 - - + -
330A LYS* 4.2 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 3.0 28.3 + - - +
84A LEU* 4.2 19.3 - - + -
102A THR* 4.5 3.8 + - - -
104A GLU* 2.9 23.8 + - - +
105A GLY* 3.7 23.5 - - - +
107A MET* 1.3 75.9 - - + +
109A ILE* 1.3 58.9 + - - +
111A GLU* 3.4 11.8 + - - +
112A GLU* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 4.2 10.8 - - - +
83A VAL* 3.6 32.5 - - + -
84A LEU* 4.0 22.0 - - + -
87A ILE* 3.6 18.1 - - + +
99A LEU* 3.9 41.3 - - + +
105A GLY 3.3 16.8 + - - +
106A CYS* 3.1 8.4 + - - +
108A ARG* 1.3 73.6 - - - +
110A VAL* 1.3 61.6 + - - +
112A GLU* 3.8 2.4 - - - +
113A GLU* 3.0 27.9 + - - +
121A VAL* 4.4 3.6 - - + -
302A ALA* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A CYS 2.8 20.8 + - - +
107A MET* 3.6 16.6 - - + +
109A ILE* 1.3 77.2 - - - +
111A GLU* 1.3 64.4 + - + +
113A GLU 3.2 1.7 + - - -
114A ILE* 3.0 38.0 + - + +
302A ALA* 3.9 29.6 - - + +
303A TRP* 4.1 26.0 - - + -
306A TYR* 4.4 4.7 - - + -
333A PRO* 4.6 2.5 - - + -
336A TYR* 3.5 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A MET* 2.8 45.9 + - + +
108A ARG* 3.7 15.3 - - - +
110A VAL* 1.3 79.1 - - + +
112A GLU* 1.3 63.7 + - + +
114A ILE* 3.5 11.2 + - + +
115A LYS* 3.5 25.5 + - - +
330A LYS* 5.7 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.8 22.7 - - + -
87A ILE* 4.0 15.6 - - + +
88A LYS* 3.8 31.7 + - - +
108A ARG* 2.9 21.0 + - + +
109A ILE* 3.8 4.9 - - - +
110A VAL 3.2 0.2 - - - -
111A GLU* 1.3 76.4 - - - +
113A GLU* 1.3 64.5 + - - +
115A LYS* 3.2 47.2 + - - +
116A VAL* 3.3 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 4.1 14.8 - - + +
109A ILE 3.0 18.7 + - - +
110A VAL 3.2 3.6 + - - +
112A GLU* 1.3 76.4 - - - +
114A ILE* 1.3 62.5 + - - +
115A LYS 3.2 0.7 + - - -
116A VAL* 3.3 5.1 + - - +
117A GLY 3.3 15.9 + - - -
118A LYS 3.5 15.1 - - - +
119A ARG* 3.4 7.1 - - - +
120A LEU* 2.9 29.3 + - + +
121A VAL* 3.0 25.3 + - + +
302A ALA* 3.4 9.0 + - - +
335A PHE* 3.8 13.7 - - + -
336A TYR* 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 3.0 33.6 + - + +
111A GLU* 3.8 11.0 - - + +
112A GLU 3.2 0.4 - - - -
113A GLU* 1.3 76.2 - - - +
115A LYS* 1.3 63.3 + - - +
117A GLY* 3.5 9.4 + - - -
333A PRO* 3.9 25.4 - - + -
335A PHE* 3.9 39.2 - - + -
336A TYR* 4.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU* 3.5 15.2 + - - +
112A GLU* 3.2 35.9 + - - +
113A GLU 3.1 0.6 - - - -
114A ILE* 1.3 76.5 - - - +
116A VAL* 1.3 57.2 + - + +
117A GLY* 2.6 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 3.5 28.9 - - + +
88A LYS* 5.0 2.9 - - - +
90A GLN* 3.5 35.4 - - + +
112A GLU* 3.3 17.2 + - - +
113A GLU 3.3 5.1 + - - +
115A LYS* 1.3 75.5 - - + +
117A GLY* 1.3 59.6 + - - +
118A LYS* 3.4 7.0 + - + +
120A LEU* 3.5 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU 3.3 5.1 + - - -
114A ILE 3.8 8.7 - - - -
115A LYS 2.6 14.2 + - - -
116A VAL* 1.3 73.3 - - - +
118A LYS* 1.3 61.6 + - - +
335A PHE* 3.7 14.5 - - - -
----------------------------------------------------------
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