Contacts of the helix formed by residues 106 - 116 (chain S) in PDB entry 6CM9
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 ASN 106 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ARG* 2.5 36.4 + - - +
95S PHE* 3.6 29.3 - - + -
102S ASP* 3.3 39.1 + - - +
103S ILE 4.3 0.4 - - - -
105S PHE* 1.3 77.8 - - - +
107S PHE* 1.3 57.7 + - - +
108S GLU* 3.2 7.0 - - - -
109S LYS* 2.9 18.6 + - + +
110S ALA* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LEU* 3.6 26.9 - - + -
11G ILE* 4.0 3.8 - - + -
51G ALA* 4.0 7.9 - - - -
54G LEU* 4.5 11.0 - - + -
55G TYR* 3.5 55.2 - + + -
58G MET* 4.1 13.7 - - + -
87G LEU* 5.5 2.9 - - + -
91G LEU* 5.5 0.4 - - + -
15S ARG 4.5 10.5 - - - +
16S LEU* 5.6 1.6 - - + -
103S ILE 3.5 20.3 + - - +
104S ILE* 3.9 10.3 - - - +
105S PHE 3.3 3.6 - - - -
106S ASN* 1.3 73.2 - - - +
108S GLU* 1.3 73.5 + - + +
110S ALA* 3.4 8.9 - - + +
111S TYR* 3.0 57.9 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G LEU* 3.5 27.9 - - + +
8G ARG* 2.5 33.8 + - - +
47G CYS* 6.1 0.3 - - - -
51G ALA* 4.1 12.8 - - + +
84G ILE* 4.2 15.8 - - + +
87G LEU* 4.4 11.4 - - + -
106S ASN* 4.3 7.6 - - - -
107S PHE* 1.3 87.5 - - + +
109S LYS* 1.3 70.1 - - + +
111S TYR* 3.8 2.1 + - - +
112S PHE* 3.1 42.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 109 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ARG* 4.5 17.3 - - - +
94S TYR* 3.4 33.0 + - + +
95S PHE* 4.9 2.9 - - + -
106S ASN* 2.9 23.5 + - + +
108S GLU* 1.3 88.0 - - + +
110S ALA* 1.3 59.5 + - - +
111S TYR 3.3 0.4 - - - -
112S PHE* 3.1 19.0 + - + +
113S ILE* 3.0 33.1 + - - +
135S ILE* 4.4 1.7 - - + +
139S ASP* 3.5 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16S LEU* 3.8 22.2 - - + -
87S TYR* 3.2 17.1 + - - +
91S LEU* 4.2 19.5 - - + -
95S PHE* 5.3 2.0 - - + -
103S ILE* 4.6 11.7 - - + -
106S ASN 2.9 7.8 + - - +
107S PHE* 3.0 18.8 + - - +
109S LYS* 1.3 75.0 - - - +
111S TYR* 1.3 60.6 + - - +
113S ILE* 3.4 2.9 + - - +
114S LEU* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 111 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G MET* 3.8 14.8 - - - +
87G LEU* 3.6 33.9 - - + -
91G LEU* 3.7 31.7 - - + +
16S LEU* 4.1 22.2 - - + +
17S GLN* 3.0 38.6 + - - +
18S LYS* 4.3 17.7 - - + -
107S PHE* 3.0 51.4 + + + +
108S GLU 3.9 5.2 - - - +
109S LYS 3.3 0.2 - - - -
110S ALA* 1.3 76.9 - - - +
112S PHE* 1.3 59.3 + - + +
114S LEU* 3.3 7.0 + - + +
115S ASP* 2.8 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G ARG* 3.3 55.2 - - + +
84G ILE* 3.7 25.4 - - + -
87G LEU* 3.6 29.2 - - + -
90G MET* 6.4 0.2 - - + -
121G LEU* 5.9 1.1 - - + -
108S GLU* 3.1 26.7 - - + -
109S LYS* 3.1 21.5 + - + +
111S TYR* 1.3 77.1 - - + +
113S ILE* 1.3 61.8 + - - +
115S ASP* 3.4 10.5 + - + +
116S GLU* 2.9 33.3 + - + +
135S ILE* 3.5 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87S TYR* 3.9 13.7 - - + -
90S LEU* 3.7 33.3 - - + +
91S LEU* 3.7 26.0 - - + +
94S TYR* 3.7 39.5 - - + -
95S PHE* 5.1 2.0 - - + -
109S LYS 3.0 17.9 + - - +
110S ALA 3.7 6.3 - - - +
112S PHE* 1.3 77.4 - - - +
114S LEU* 1.3 62.3 + - - +
116S GLU* 3.1 7.1 + - - +
117S PHE* 3.0 22.3 + - - +
132S VAL* 6.3 0.4 - - + -
135S ILE* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5S ILE* 3.7 28.5 - - + -
16S LEU* 3.8 22.2 - - + -
18S LYS* 3.8 35.4 - - + -
20S TYR* 4.1 6.5 - - - +
87S TYR* 3.6 30.0 - - + +
110S ALA 3.0 16.8 + - - +
111S TYR* 3.3 8.7 + - + +
113S ILE* 1.3 76.6 - - - +
115S ASP* 1.3 56.7 + - - +
117S PHE* 4.4 1.3 - - + +
118S ILE* 2.8 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G LEU* 4.6 2.8 - - - +
90G MET* 3.3 19.9 - - + +
121G LEU* 6.1 4.5 - - + -
124G CYS* 3.6 26.4 - - - +
128G CYS* 4.1 0.5 - - - -
156G LYS* 3.6 6.6 + - - -
18S LYS* 3.3 29.7 + - - -
111S TYR* 2.8 26.9 + - - +
112S PHE* 3.6 11.0 - - + +
113S ILE 3.2 0.4 - - - -
114S LEU* 1.3 76.0 - - - +
116S GLU* 1.3 65.4 + - - +
117S PHE 3.3 0.9 - - - -
118S ILE 4.1 7.7 - - - +
119S ILE* 3.3 19.0 - - - +
124S GLN* 3.3 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G ARG* 5.0 6.9 + - - -
120G GLY 5.7 2.4 - - - -
121G LEU* 5.4 7.4 - - - +
152G TYR* 2.5 39.5 + - - -
155G LYS* 5.2 1.9 + - - -
156G LYS* 4.2 5.4 + - - -
90S LEU* 6.4 0.2 - - + -
112S PHE* 2.9 21.4 + - + +
113S ILE* 3.1 6.2 + - - +
115S ASP* 1.3 79.4 - - - +
117S PHE* 1.3 56.9 + - - +
124S GLN* 3.1 19.6 + - - +
125S GLU* 4.4 4.7 - - - +
131S ALA* 4.2 27.9 - - + +
134S ALA* 4.0 8.4 - - - +
135S ILE* 4.0 25.6 - - + +
138S SER* 5.0 6.2 + - - -
----------------------------------------------------------
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