Contacts of the helix formed by residues 87 - 103 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F LEU* 4.3 14.8 - - + +
86F GLY* 1.3 66.1 - - - -
88F GLU* 1.3 62.7 + - - +
89F ILE* 2.9 24.4 + - - +
90F ALA* 3.1 26.7 + - + +
91F ILE* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F THR* 2.6 32.2 + - - +
82F THR 3.8 14.4 - - - +
83F SER* 3.2 28.1 + - - -
86F GLY 2.9 15.0 + - - +
87F ASP* 1.3 73.6 + - - +
89F ILE* 1.3 53.8 + - - +
91F ILE* 4.5 4.7 - - - -
92F GLY* 2.7 29.7 + - - -
110F TYR* 4.3 4.7 + - - +
127F MET* 4.2 11.4 - - - +
130F PRO* 4.9 16.6 - - + +
131F LYS* 3.0 29.8 + - + +
134F VAL* 3.5 5.6 - - - +
1353F NAP 4.1 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F ASP* 2.9 9.9 + - - +
88F GLU* 1.3 75.8 - - - +
90F ALA* 1.3 59.0 + - - +
91F ILE 3.2 1.3 - - - -
93F LYS* 2.6 68.2 + - + +
130F PRO* 3.6 42.0 - - + +
133F THR* 4.0 21.1 - - + +
134F VAL* 3.7 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F LEU* 5.1 7.9 - - + -
62F ASN* 5.6 5.2 - - - +
87F ASP* 3.1 28.2 + - + +
89F ILE* 1.3 80.7 - - - +
91F ILE* 1.3 57.9 + - - +
93F LYS* 3.6 5.5 + - - +
94F ASP* 2.9 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F LEU* 3.7 34.3 - - + +
61F LEU* 3.6 40.8 - - + +
62F ASN 4.9 0.9 - - - +
67F MET* 4.3 2.7 - - + -
81F THR* 4.1 11.9 - - + -
85F ALA* 3.6 27.6 - - + +
86F GLY 4.1 2.7 - - - +
87F ASP 3.1 25.0 + - - +
88F GLU* 4.2 2.0 - - - +
89F ILE 3.2 0.4 - - - -
90F ALA* 1.3 76.7 - - - +
92F GLY* 1.3 59.7 + - - +
94F ASP* 3.3 6.3 + - - +
95F LEU* 2.9 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ILE* 5.9 0.4 - - - +
81F THR* 5.1 2.0 - - - -
88F GLU 2.7 26.4 + - - -
89F ILE 3.1 1.3 + - - -
91F ILE* 1.3 76.7 - - - +
93F LYS* 1.3 58.5 + - - +
95F LEU* 4.0 7.9 - - - +
96F ALA* 3.3 21.7 + - - +
108F TYR* 4.3 2.3 + - - -
110F TYR* 4.7 6.7 - - - -
134F VAL* 3.6 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ILE* 2.6 43.9 + - + +
90F ALA* 4.0 5.8 - - - +
92F GLY* 1.3 71.5 - - - +
94F ASP* 1.3 67.4 + - - +
96F ALA* 3.3 2.4 + - - +
97F ASP* 2.9 31.1 + - - +
133F THR* 5.2 9.5 - - - +
134F VAL* 5.1 3.1 - - + +
137F TYR* 3.9 52.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ASN* 4.5 18.0 + - - -
63F ASN 5.0 0.2 + - - -
64F VAL* 4.0 21.9 - - + +
67F MET* 3.4 26.3 - - + +
90F ALA* 2.9 22.2 + - - +
91F ILE* 4.3 0.7 - - - -
93F LYS* 1.3 78.3 - - - +
95F LEU* 1.3 57.4 + - - +
97F ASP* 3.0 12.0 + - - +
98F ALA* 2.8 28.8 + - - +
101F ARG* 5.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F VAL* 4.1 27.6 - - + -
60F LEU* 4.1 4.7 - - + -
67F MET* 3.6 30.3 - - + -
70F LEU* 4.7 3.1 - - + -
71F PHE* 3.3 25.8 - - + -
79F ILE* 3.9 23.8 - - + -
81F THR* 4.3 8.5 - - + -
91F ILE* 2.9 36.7 + - + +
92F GLY* 4.0 3.4 - - - +
94F ASP* 1.3 75.5 - - - +
96F ALA* 1.3 58.7 + - - +
98F ALA 3.0 1.6 + - - -
99F ALA* 2.8 28.6 + - - +
108F TYR* 3.8 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F GLY 3.3 16.0 + - - +
93F LYS 3.6 4.7 - - - +
94F ASP 3.3 0.4 - - - -
95F LEU* 1.3 79.2 - - - +
97F ASP* 1.3 56.2 + - - +
99F ALA* 3.6 0.4 + - - -
100F LYS* 3.1 21.7 + - - +
108F TYR* 3.4 13.1 + - - +
137F TYR* 4.0 9.2 - - + -
138F VAL* 4.2 10.8 - - + -
141F LEU* 3.4 30.1 - - + +
143F LEU* 3.5 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F LYS* 2.9 19.5 + - - +
94F ASP* 3.0 13.6 + - - +
96F ALA* 1.3 75.0 - - - +
98F ALA* 1.3 63.8 + - - +
100F LYS* 3.4 4.9 + - - +
101F ARG* 2.9 42.6 + - - +
137F TYR* 2.8 31.6 + - - -
141F LEU* 3.7 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F MET* 3.7 23.8 - - + +
68F ASP* 4.2 5.2 - - - +
71F PHE* 3.2 28.7 - - + +
94F ASP 2.8 12.7 + - - +
95F LEU 3.4 2.7 - - - +
97F ASP* 1.3 75.5 - - - +
99F ALA* 1.3 65.3 + - - +
101F ARG* 3.1 22.9 + - - +
102F ALA* 2.9 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F PHE* 3.4 21.4 - - + -
95F LEU 2.8 15.8 + - - +
96F ALA 3.6 4.7 - - - +
98F ALA* 1.3 76.2 - - - +
100F LYS* 1.3 62.7 + - - +
102F ALA* 3.1 13.2 + - - +
103F GLY* 3.3 8.5 + - - -
105F ILE* 4.0 16.3 - - + +
108F TYR* 3.6 31.2 - - + -
143F LEU* 4.3 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E LEU* 3.7 24.8 - - - +
96F ALA 3.1 15.1 + - - +
97F ASP* 3.7 7.4 - - - +
98F ALA 3.2 0.2 - - - -
99F ALA* 1.3 79.1 - - - +
101F ARG* 1.3 62.1 + - - +
103F GLY* 3.0 15.6 + - - -
141F LEU* 2.8 53.3 + - + +
142F GLY 5.9 0.2 - - - -
143F LEU* 3.9 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F VAL* 3.6 25.2 - - - +
68F ASP* 3.3 30.0 + - - +
94F ASP 5.0 1.2 + - - -
97F ASP* 2.9 30.0 + - - +
98F ALA* 3.1 22.1 + - - +
100F LYS* 1.3 73.3 - - - +
102F ALA* 1.3 66.9 + - - +
103F GLY* 3.0 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F ASP 5.9 0.2 - - - +
71F PHE* 3.7 34.5 - - + +
72F GLU* 5.5 1.1 - - - -
98F ALA 2.9 12.2 + - - +
99F ALA* 3.1 11.0 + - - +
101F ARG* 1.3 76.7 - - - +
103F GLY* 1.3 57.5 + - - +
104F THR* 2.9 25.5 + - - +
105F ILE* 4.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F ALA 3.3 3.6 + - - -
100F LYS* 3.0 14.8 + - - -
101F ARG 3.0 5.2 - - - -
102F ALA* 1.3 77.8 - - - +
104F THR* 1.3 60.8 + - - +
105F ILE 3.6 4.2 - - - +
----------------------------------------------------------
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