Contacts of the helix formed by residues 93 - 107 (chain G) in PDB entry 2R9R
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 93 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G GLU 3.3 16.4 + - - -
90G TYR 3.1 6.7 + - - -
92G ALA* 1.3 75.4 - - - +
94G LYS* 1.3 62.3 + - - +
95G ALA 3.3 2.5 - - - -
96G GLU* 3.4 9.0 + - - +
97G VAL* 3.3 16.7 + - - +
146G ARG* 3.4 35.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLY* 3.8 23.9 + - - +
91G ALA* 3.2 24.2 + - + +
92G ALA* 3.3 4.4 - - + +
93G GLY* 1.3 75.9 - - - +
95G ALA* 1.3 64.2 + - - +
96G GLU 3.2 0.2 - - - -
97G VAL* 3.7 10.4 - - + +
98G VAL* 2.9 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G THR* 3.9 7.1 - - - +
60G PHE* 3.6 36.7 + - + +
86G THR* 3.7 12.1 - - - +
90G TYR* 3.4 35.5 + - + +
91G ALA* 4.2 0.2 - - - +
93G GLY 3.3 0.8 - - - -
94G LYS* 1.3 78.0 - - - +
96G GLU* 1.3 58.0 + - - +
98G VAL* 3.8 1.7 - - - +
99G LEU* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G THR* 3.6 25.1 - - + +
87G ALA 3.8 11.7 - - - +
88G GLU* 3.4 7.8 + - - -
93G GLY* 3.4 8.6 + - - +
94G LYS 3.2 0.4 - - - -
95G ALA* 1.3 79.5 - - - +
97G VAL* 1.3 55.7 + - - +
99G LEU* 4.3 0.4 - - - -
100G GLY 3.0 24.6 + - - -
117G THR* 2.8 19.9 + - - -
143G SER* 2.6 28.9 + - - -
146G ARG* 2.7 50.4 + - + -
147G LEU* 3.6 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G GLY 3.3 15.1 + - - +
94G LYS* 3.3 16.0 + - + +
96G GLU* 1.3 76.3 - - - +
98G VAL* 1.3 60.7 + - + +
100G GLY* 3.9 0.3 - - - -
101G ASN* 2.9 47.3 + - - +
146G ARG* 3.6 34.5 - - + +
148G GLN* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G PHE* 3.7 21.8 - - + -
61G GLY* 3.8 17.5 - - - +
66G ASP* 3.6 33.4 - - + +
69G ALA* 3.9 17.7 - - + -
94G LYS* 2.9 22.3 + - + +
95G ALA 3.8 2.9 - - - +
97G VAL* 1.3 79.6 - - + +
99G LEU* 1.3 63.1 + - - +
101G ASN* 3.2 8.5 + - - +
102G ILE* 3.0 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G THR* 4.6 7.9 - - + -
60G PHE* 4.2 19.1 - - + -
73G MET* 3.4 39.7 - - + -
84G PHE* 4.5 15.7 - - + +
86G THR* 4.0 23.1 - - + -
95G ALA 2.9 18.7 + - - +
96G GLU 3.7 3.6 - - - +
98G VAL* 1.3 76.7 - - - +
100G GLY* 1.3 61.1 + - - +
102G ILE* 3.3 5.5 + - - +
103G ILE* 3.2 30.5 + - + +
115G ILE* 4.5 12.3 - - + -
147G LEU* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G GLU 3.0 15.6 + - - -
97G VAL 3.9 1.1 - - - -
99G LEU* 1.3 74.2 - - - +
101G ASN* 1.3 61.5 + - - +
103G ILE* 3.9 8.8 - - - +
104G LYS* 3.0 30.8 + - - +
146G ARG 5.0 0.2 - - - -
147G LEU* 3.4 31.5 - - - +
148G GLN* 4.2 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G VAL* 2.9 39.7 + - - +
98G VAL* 3.6 8.2 - - - +
100G GLY* 1.3 76.6 - - - +
102G ILE* 1.3 58.3 + - + +
104G LYS* 3.9 5.9 + - - +
105G LYS* 3.1 28.9 + - - +
148G GLN* 2.9 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G PHE* 3.9 13.9 - - + -
66G ASP* 4.7 2.0 - - + +
69G ALA* 3.6 19.5 - - + +
70G GLU* 3.5 45.8 - - + +
73G MET* 3.8 26.7 - - + -
98G VAL* 3.0 23.3 + - + +
99G LEU 3.5 6.7 - - - +
100G GLY 3.2 0.4 - - - -
101G ASN* 1.3 76.9 - - + +
103G ILE* 1.3 61.2 + - - +
105G LYS* 3.3 4.8 + - - +
106G LYS* 2.8 49.9 + - + +
108G TRP* 4.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G MET* 4.2 14.8 - - + -
99G LEU* 3.2 28.6 + - + +
100G GLY* 3.9 8.1 - - - +
101G ASN 3.5 0.2 - - - -
102G ILE* 1.3 75.1 - - - +
104G LYS* 1.3 65.8 + - - +
107G GLY* 3.1 21.1 + - - -
108G TRP* 3.8 20.8 + - + +
110G ARG* 5.8 2.9 - - - -
113G LEU* 3.9 26.0 - - + -
115G ILE* 3.8 31.9 - - + -
147G LEU* 5.6 0.4 - - + -
149G LEU* 4.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G GLY 3.0 17.7 + - - +
101G ASN* 3.9 6.0 + - - +
103G ILE* 1.3 79.9 - - - +
105G LYS* 1.3 62.1 + - - +
107G GLY* 3.4 11.5 + - - -
148G GLN* 3.0 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G GLU* 2.8 39.3 + - - +
101G ASN 3.1 19.0 + - - +
102G ILE* 3.8 4.7 - - - +
104G LYS* 1.3 76.9 - - - +
106G LYS* 1.3 67.3 + - + +
107G GLY* 3.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G GLU* 4.2 26.0 + - + +
74G THR* 3.7 31.2 + - - +
102G ILE* 2.8 26.3 + - + +
103G ILE 4.2 0.4 - - - +
105G LYS* 1.3 81.2 - - + +
107G GLY* 1.3 62.6 + - - +
108G TRP* 3.2 54.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 107 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G ILE 3.1 10.0 + - - -
104G LYS 3.4 7.1 + - - -
105G LYS 3.2 4.6 + - - -
106G LYS* 1.3 77.3 - - - +
108G TRP* 1.3 66.9 + - - +
109G ARG* 3.5 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