Contacts of the helix formed by residues 106 - 125 (chain A) in PDB entry 1TE6
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 GLY 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.9 3.4 - - - -
48A LEU* 3.8 13.0 - - - -
97A ASP* 4.2 0.2 + - - -
102A LYS* 2.9 19.3 + - - -
103A SER* 4.4 1.5 - - - -
104A LYS 3.5 1.6 - - - +
105A PHE* 1.3 84.0 - - - +
107A ALA* 1.3 65.2 + - - -
108A ASN* 3.1 13.0 - - - -
109A ALA 3.2 7.8 + - - -
110A ILE* 3.2 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA* 3.5 30.3 - - + +
46A LEU 2.7 22.3 + - - +
47A GLU* 5.2 0.4 - - - -
102A LYS* 3.5 22.3 + - + -
106A GLY* 1.3 72.1 - - - -
108A ASN* 1.3 57.1 + - - +
110A ILE 4.6 0.4 - - - +
111A LEU* 2.9 33.7 + - - +
344A ASN* 4.5 9.6 - - + +
347A GLY* 3.9 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 5.6 1.3 + - - +
19A VAL* 3.9 14.8 - - + +
34A VAL* 3.4 32.5 - - + +
46A LEU 4.1 0.8 + - - -
47A GLU* 4.3 16.0 - - + +
48A LEU* 3.1 46.2 + - - +
61A VAL* 3.8 17.4 - - - +
64A ALA* 3.8 10.1 - - - +
106A GLY* 3.6 8.0 - - - -
107A ALA* 1.3 73.3 - - - +
109A ALA* 1.3 65.5 + - - +
112A GLY* 3.2 16.8 + - - -
344A ASN* 6.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 4.8 3.1 - - - -
21A VAL* 4.9 0.2 - - - +
64A ALA* 3.6 22.0 - - + +
67A HIS* 4.8 0.7 - - + -
68A ILE* 2.9 36.9 - - + +
72A ILE* 4.6 0.2 - - + -
105A PHE* 3.3 32.1 - - + +
106A GLY 3.2 2.7 + - - +
108A ASN* 1.3 79.5 + - - +
110A ILE* 1.3 66.7 + - - +
112A GLY* 3.3 9.5 + - - -
113A VAL 3.4 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 4.3 9.4 - - + -
90A ASP 5.5 0.7 - - - +
93A MET* 3.8 37.7 - - + +
94A LEU* 4.8 4.3 - - + -
97A ASP* 3.9 25.1 - - + +
102A LYS* 3.6 40.6 - - + -
105A PHE* 4.3 11.2 - - + -
106A GLY 3.2 13.9 + - - +
107A ALA 4.1 1.3 - - - +
109A ALA* 1.3 76.5 - - - +
111A LEU* 1.3 57.1 + - - +
113A VAL* 3.3 5.2 + - - +
114A SER* 2.9 24.9 + - - -
347A GLY 3.4 15.9 - - - +
348A SER* 4.6 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.1 12.3 - - + -
35A PRO* 4.6 1.8 - - + -
107A ALA 2.9 18.8 + - - +
108A ASN 4.4 2.5 - - - +
110A ILE* 1.3 74.1 - - - +
112A GLY* 1.3 66.9 + - - +
114A SER* 4.1 2.9 - - - -
115A LEU* 2.9 54.1 + - + +
343A VAL* 3.7 24.5 - - + -
344A ASN* 3.4 42.6 - - + +
347A GLY* 3.2 22.8 + - - +
348A SER* 4.0 11.2 - - - -
349A VAL 4.3 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 4.7 0.9 - - - -
21A VAL* 3.5 29.8 - - - +
32A ALA* 4.3 6.3 - - - +
34A VAL* 3.5 20.1 - - - +
108A ASN 3.2 12.0 + - - -
109A ALA 3.8 2.0 - - - -
110A ILE 3.3 0.8 - - - -
111A LEU* 1.3 76.3 - - - +
113A VAL* 1.3 60.7 + - - +
115A LEU* 3.9 5.3 - - - +
116A ALA* 3.3 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.6 11.4 - - + -
21A VAL* 4.2 12.8 - - + -
23A LEU* 4.9 1.6 - - + -
68A ILE* 3.1 48.7 - - + -
72A ILE* 4.2 6.1 - - + -
76A LEU* 3.5 32.8 - - + -
93A MET* 3.7 9.4 - - - -
109A ALA 3.4 0.2 + - - -
110A ILE 3.3 6.0 + - - +
111A LEU 3.2 0.4 - - - -
112A GLY* 1.3 76.1 - - - +
114A SER* 1.3 60.0 + - - +
116A ALA* 3.1 2.4 + - - +
117A VAL* 2.8 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 3.2 18.2 + - - +
90A ASP* 2.6 29.7 + - - -
93A MET* 3.8 5.6 - - - +
110A ILE 2.9 17.3 + - - -
111A LEU* 3.2 9.8 + - - -
113A VAL* 1.3 78.0 - - - +
115A LEU* 1.3 56.6 + - - +
117A VAL* 3.4 2.7 + - - +
118A CYS* 3.0 24.4 + - - +
348A SER* 4.3 3.4 - - - -
349A VAL* 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 3.4 18.8 - - + -
33A ALA 3.7 25.8 - - - +
34A VAL* 4.6 1.8 - - + -
35A PRO* 5.3 1.8 - - + -
111A LEU* 2.9 46.0 + - + +
112A GLY* 3.9 1.1 - - - +
114A SER* 1.3 75.2 - - - +
116A ALA* 1.3 64.9 + - - +
118A CYS* 3.2 4.8 + - - +
119A LYS* 3.2 26.3 + - - +
343A VAL* 5.0 8.3 - - + -
349A VAL* 3.8 13.7 - - + -
377A ASP* 5.1 2.9 - - - +
379A PHE* 3.6 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.0 18.4 - - + +
23A LEU* 3.8 16.8 - - + +
30A PHE* 3.7 23.8 - - - +
32A ALA* 3.8 7.6 - - - +
112A GLY 3.3 11.4 + - - +
113A VAL 3.1 7.5 + - - +
115A LEU* 1.3 77.6 - - - +
117A VAL* 1.3 63.2 + - - +
119A LYS* 3.3 7.6 + - - +
120A ALA* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE* 4.8 2.7 - - + -
23A LEU* 3.4 23.8 - - + -
76A LEU* 4.7 6.3 - - + -
83A VAL* 3.6 13.7 - - + +
86A GLN* 3.8 18.2 - - - +
89A LEU* 3.5 37.9 - - + -
93A MET* 5.3 1.8 - - + -
113A VAL* 2.8 32.7 + - + +
114A SER* 3.4 8.1 - - - +
116A ALA* 1.3 77.2 - - - +
118A CYS* 1.3 57.4 + - - +
120A ALA* 3.3 4.6 + - - +
121A GLY 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 3.0 21.7 + - - +
114A SER 3.0 10.5 + - - +
115A LEU 3.2 8.5 + - - +
117A VAL* 1.3 77.8 - - - +
119A LYS* 1.3 62.6 + - - +
121A GLY 3.2 0.7 + - - -
122A ALA 3.1 18.9 + - - -
129A LEU* 3.8 3.8 - - - +
132A HIS* 3.3 24.1 - - - -
133A ILE* 3.0 38.1 - - - -
136A LEU* 4.0 5.4 - - - -
349A VAL* 4.3 5.4 - - + -
379A PHE* 3.8 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 3.8 20.4 - - + -
31A ARG 2.9 34.8 + - - +
32A ALA* 3.6 10.6 - - + +
115A LEU 3.2 12.1 + - - +
116A ALA* 3.3 5.8 + - - +
118A CYS* 1.3 76.5 - - - +
120A ALA* 1.3 61.2 + - - +
122A ALA* 3.5 4.7 + - - +
123A ALA* 3.4 15.6 + - - +
129A LEU* 3.8 27.4 - - + -
377A ASP* 2.9 26.6 + - - +
378A THR* 5.0 2.2 + - - +
379A PHE* 3.9 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.8 18.6 - - + -
25A THR* 4.0 3.6 + - + -
27A LYS* 5.3 1.0 - - - +
30A PHE* 3.5 34.5 - - + -
83A VAL* 3.5 18.9 - - + +
116A ALA 3.0 17.0 + - - +
117A VAL 3.7 4.3 - - - +
119A LYS* 1.3 73.9 - - - +
121A GLY* 1.3 59.9 + - - +
123A ALA* 3.3 4.0 + - - +
124A GLU* 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 3.4 32.9 - - - +
84A VAL* 3.9 7.1 - - - +
117A VAL 2.9 10.5 + - - -
118A CYS 3.2 3.7 + - - -
120A ALA* 1.3 75.1 - - - +
122A ALA* 1.3 63.9 - - - +
124A GLU* 3.1 11.6 + - - +
125A ARG* 3.2 13.0 + - - +
132A HIS* 3.7 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A CYS 3.1 8.5 + - - +
119A LYS 3.7 8.7 - - - +
120A ALA 3.3 0.4 - - - -
121A GLY* 1.3 75.7 - - - +
123A ALA* 1.3 61.2 + - - +
125A ARG* 3.3 4.4 + - - +
126A GLU 3.2 4.5 + - - -
127A LEU* 3.0 39.2 + - - +
129A LEU* 3.8 18.8 - - + +
132A HIS* 3.4 35.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 3.6 23.6 + - + +
30A PHE* 3.4 39.9 - - + -
119A LYS 3.4 3.8 + - - +
120A ALA 3.3 3.1 + - - +
121A GLY 3.2 0.4 - - - -
122A ALA* 1.3 76.6 - - - +
124A GLU* 1.3 65.4 + - - +
126A GLU* 3.0 14.5 + - - +
127A LEU 4.7 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SER* 4.2 18.1 + - - -
25A THR* 5.1 4.7 + - - -
26A ALA* 5.8 2.8 + - - +
27A LYS* 4.0 28.6 - - - +
82A SER* 4.0 9.0 - - - +
83A VAL* 3.9 8.7 - - + +
84A VAL* 3.6 23.1 - - + -
120A ALA 2.9 13.1 + - - +
121A GLY 3.1 9.8 + - - +
123A ALA* 1.3 78.9 - - - +
125A ARG* 1.3 57.6 + - + +
126A GLU* 3.2 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 3.4 51.5 + - + +
85A GLU* 5.1 4.0 + - - -
121A GLY 3.2 8.4 + - - +
122A ALA 4.0 3.4 - - - +
123A ALA 3.2 0.2 - - - -
124A GLU* 1.3 75.2 - - + +
126A GLU* 1.3 73.6 + - - +
127A LEU* 3.3 19.3 - - + +
132A HIS* 4.3 16.0 + - - +
135A GLN* 3.6 30.4 + - - +
136A LEU* 5.9 3.1 - - - +
----------------------------------------------------------
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