Contacts of the helix formed by residues 87 - 103 (chain G) in PDB entry 2VUU
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 ASP 87 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G LEU* 4.1 17.4 - - + +
86G GLY* 1.3 66.5 - - - -
88G GLU* 1.3 63.7 + - - +
89G ILE* 3.0 23.5 + - - +
90G ALA* 3.2 25.3 + - + +
91G ILE* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G THR* 2.9 35.7 + - - +
82G THR 3.7 15.5 - - - +
83G SER* 3.4 31.9 + - - -
86G GLY 3.1 9.2 + - - +
87G ASP* 1.3 72.0 + - - +
89G ILE* 1.3 54.2 + - - +
91G ILE* 4.4 5.8 - - + -
92G GLY* 2.7 30.4 + - - -
110G TYR* 5.5 0.7 - - - +
126G PRO 5.5 0.7 - - - +
127G MET* 4.5 10.9 - - - +
130G PRO* 5.0 16.5 - - + +
131G LYS* 3.0 33.5 + - + +
134G VAL* 3.6 7.1 - - + +
1353G NAP 3.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G ASP* 3.0 11.0 + - - +
88G GLU* 1.3 74.7 - - - +
90G ALA* 1.3 59.0 + - - +
92G GLY 3.8 0.2 - - - -
93G LYS* 2.8 66.2 + - + +
130G PRO* 3.5 41.7 - - + +
133G THR* 4.1 23.8 - - + +
134G VAL* 3.8 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G LEU* 4.9 9.0 - - + -
62G ASN* 5.4 5.8 - - - +
87G ASP* 3.2 32.0 + - + +
89G ILE* 1.3 80.0 - - - +
91G ILE* 1.3 57.4 + - - +
93G LYS* 3.4 6.2 + - - +
94G ASP* 2.9 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G LEU* 3.9 22.4 - - + +
61G LEU* 3.4 50.5 - - + +
62G ASN 4.8 0.9 - - - +
67G MET* 4.5 1.6 - - + -
81G THR* 3.9 15.0 - - + -
85G ALA* 4.2 18.2 - - + +
86G GLY 4.4 1.6 - - - -
87G ASP 3.0 24.9 + - - +
88G GLU* 4.1 3.1 - - + +
90G ALA* 1.3 76.7 - - + +
92G GLY* 1.3 59.5 + - - +
94G ASP* 3.2 7.3 + - - +
95G LEU* 2.8 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G ILE* 5.9 0.4 - - - -
81G THR* 4.7 5.2 - - - -
88G GLU 2.7 24.6 + - - -
89G ILE 3.8 0.4 - - - -
91G ILE* 1.3 73.6 - - - +
93G LYS* 1.3 57.8 + - - +
95G LEU* 3.5 10.0 + - - +
96G ALA* 3.0 29.5 + - - +
108G TYR* 4.5 1.7 + - - -
110G TYR* 5.2 2.5 - - - -
134G VAL* 3.8 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G ILE* 2.8 43.1 + - + +
90G ALA* 3.6 6.1 - - - +
92G GLY* 1.3 73.9 - - - +
94G ASP* 1.3 67.2 + - - +
96G ALA* 3.3 1.7 + - - +
97G ASP* 2.9 32.5 + - - +
133G THR* 5.0 9.9 - - - +
134G VAL* 5.4 2.9 - - + -
137G TYR* 3.7 55.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ASN* 4.6 16.1 + - - -
64G VAL* 3.9 23.0 - - + +
67G MET* 3.5 25.5 - - + +
90G ALA* 2.9 22.7 + - - +
91G ILE* 3.6 3.3 - - - +
93G LYS* 1.3 77.5 - - - +
95G LEU* 1.3 56.1 + - - +
97G ASP* 3.0 13.6 + - - +
98G ALA* 2.8 28.9 + - - +
101G ARG* 4.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G VAL* 4.1 21.5 - - + -
60G LEU* 4.5 8.5 - - + -
66G LEU* 6.5 0.4 - - + -
67G MET* 3.5 28.9 - - + -
70G LEU* 4.8 1.6 - - + -
71G PHE* 3.4 24.2 - - + -
79G ILE* 3.9 22.9 - - + -
81G THR* 4.0 7.2 - - + -
91G ILE* 2.8 44.6 + - + +
92G GLY* 3.8 4.9 - - - +
94G ASP* 1.3 72.6 - - - +
96G ALA* 1.3 57.0 + - - +
98G ALA* 3.1 4.3 + - - +
99G ALA* 2.8 28.1 + - - +
108G TYR* 3.8 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G GLY 3.0 17.9 + - - +
93G LYS 3.7 3.8 - - - +
95G LEU* 1.3 76.0 - - - +
97G ASP* 1.3 57.2 + - - +
99G ALA 3.4 0.3 + - - -
100G LYS* 3.0 27.9 + - - +
108G TYR* 3.6 9.3 + - - +
137G TYR* 4.1 11.4 - - + -
138G VAL* 4.2 20.4 - - + -
141G LEU* 3.5 21.2 - - + +
143G LEU* 3.7 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G LYS* 2.9 23.5 + - - +
94G ASP* 3.3 15.9 - - - +
96G ALA* 1.3 75.4 - - - +
98G ALA* 1.3 60.3 + - - +
100G LYS* 3.3 4.7 + - - +
101G ARG* 2.9 48.5 + - - +
137G TYR* 2.7 34.0 + - - -
141G LEU* 3.4 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G MET* 3.7 23.6 - - + +
68G ASP* 4.4 5.8 - - - +
71G PHE* 3.4 23.1 - - + +
94G ASP 2.8 16.5 + - - +
95G LEU 3.4 8.3 - - - +
97G ASP* 1.3 73.4 - - - +
99G ALA* 1.3 58.8 + - - +
101G ARG* 3.3 22.0 + - - +
102G ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G PHE* 3.7 22.9 - - + -
95G LEU 2.8 11.2 + - - +
96G ALA 3.7 2.9 - - - +
98G ALA* 1.3 75.5 - - - +
100G LYS* 1.3 66.1 + - - +
102G ALA* 3.4 11.1 + - - +
103G GLY* 3.4 8.1 + - - -
105G ILE* 4.2 16.6 - - + +
108G TYR* 3.5 37.2 - - + -
143G LEU* 4.3 6.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G ALA 3.0 17.2 + - - +
97G ASP* 3.6 7.9 - - - +
98G ALA 3.3 0.2 - - - -
99G ALA* 1.3 75.8 - - - +
101G ARG* 1.3 64.6 + - - +
103G GLY* 2.9 17.0 + - - -
141G LEU* 3.4 54.1 - - + +
143G LEU* 3.9 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G VAL* 3.4 28.3 - - - +
68G ASP* 3.6 15.9 + - - +
94G ASP* 4.4 1.2 + - - +
97G ASP* 2.9 30.4 + - - +
98G ALA* 3.3 30.8 - - - +
100G LYS* 1.3 77.2 - - - +
102G ALA* 1.3 61.3 + - - +
103G GLY* 3.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ASP 5.9 0.7 - - - +
71G PHE* 3.7 27.8 - - + +
72G GLU* 5.5 1.3 - - - -
98G ALA 3.0 13.8 + - - +
99G ALA* 3.5 10.1 - - - +
100G LYS 3.2 0.4 - - - -
101G ARG* 1.3 76.0 - - - +
103G GLY* 1.3 59.0 + - - +
104G THR* 2.9 31.9 + - - +
105G ILE* 5.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G ALA 3.4 4.3 + - - -
100G LYS 2.9 16.8 + - - -
101G ARG 3.1 1.5 - - - -
102G ALA* 1.3 76.2 - - - +
104G THR* 1.3 59.3 + - - +
105G ILE 3.6 4.8 - - - +
----------------------------------------------------------
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