Contacts of the helix formed by residues 87 - 103 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H LEU* 4.4 11.8 - - + +
86H GLY* 1.3 65.8 - - - -
88H GLU* 1.3 62.3 + - - +
89H ILE* 3.0 19.6 + - - +
90H ALA* 3.0 27.7 + - + +
91H ILE* 3.2 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H THR* 2.8 31.9 + - - +
82H THR* 3.4 24.0 - - - +
83H SER* 3.2 25.5 + - - -
86H GLY 2.7 8.8 + - - +
87H ASP* 1.3 72.0 + - - +
89H ILE* 1.3 58.7 + - + +
91H ILE* 3.9 5.3 - - + +
92H GLY* 2.8 27.6 + - - -
110H TYR* 4.9 1.4 + - - +
126H PRO 5.2 1.0 - - - +
127H MET* 4.2 15.2 - - - +
130H PRO* 4.9 15.4 - - + +
131H LYS* 3.5 32.1 - - + +
134H VAL* 3.7 6.7 - - + +
1353H NAP 4.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H ASP* 3.0 10.5 + - - +
88H GLU* 1.3 76.2 - - - +
90H ALA* 1.3 61.1 + - - +
93H LYS* 2.9 62.4 + - + +
130H PRO* 3.4 45.5 - - + +
133H THR* 3.7 24.7 - - + +
134H VAL* 3.8 8.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H LEU* 4.6 10.8 - - + -
62H ASN* 5.4 5.4 - - - +
87H ASP* 3.0 30.7 + - + +
89H ILE* 1.3 78.1 - - - +
91H ILE* 1.3 61.7 + - - +
93H LYS* 4.0 6.0 - - - +
94H ASP* 3.1 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H LEU* 3.9 23.6 - - + -
61H LEU* 4.1 33.0 - - + +
62H ASN 6.1 0.4 - - - +
67H MET* 4.0 8.7 - - + -
81H THR* 4.4 9.9 - - + -
82H THR 5.1 1.3 - - - +
85H ALA* 4.2 20.9 - - + -
86H GLY* 3.6 21.1 - - - +
87H ASP 3.2 17.7 + - - +
88H GLU* 3.9 6.7 - - + +
90H ALA* 1.3 74.7 - - - +
92H GLY* 1.3 65.7 + - - +
94H ASP* 3.1 5.1 + - - +
95H LEU* 2.9 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H ILE* 5.9 0.4 - - - +
81H THR* 5.0 5.8 - - - -
88H GLU 2.8 23.6 + - - -
89H ILE 3.4 0.6 + - - -
91H ILE* 1.3 75.4 - - - +
93H LYS* 1.3 59.3 + - - +
95H LEU* 3.6 9.7 + - - +
96H ALA* 3.2 23.0 + - - +
108H TYR* 4.6 1.7 + - - -
110H TYR* 5.1 1.6 - - - -
134H VAL* 3.7 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ILE* 2.9 45.0 + - + +
90H ALA* 4.0 6.1 - - - +
92H GLY* 1.3 74.6 - - - +
94H ASP* 1.3 62.3 + - - +
96H ALA* 3.3 2.6 + - - +
97H ASP* 2.9 37.9 + - - +
133H THR* 4.6 11.8 + - - +
134H VAL* 5.4 3.1 - - + -
137H TYR* 2.8 65.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H ASN* 4.7 19.4 + - - -
63H ASN 5.3 0.2 + - - -
64H VAL* 4.3 19.5 - - + +
67H MET* 3.5 23.4 - - + +
90H ALA* 3.1 22.4 + - - +
91H ILE* 3.1 5.2 + - - +
93H LYS* 1.3 80.9 - - - +
95H LEU* 1.3 57.7 + - - +
97H ASP* 3.2 12.4 + - - +
98H ALA* 2.8 29.6 + - - +
101H ARG* 3.8 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H VAL* 4.1 19.1 - - + -
60H LEU* 3.8 11.4 - - + -
67H MET* 3.5 35.4 - - + -
70H LEU* 5.0 1.8 - - + -
71H PHE* 3.3 19.8 - - + -
79H ILE* 3.8 27.4 - - + -
81H THR* 4.1 9.0 - - + -
91H ILE* 2.9 33.8 + - + +
92H GLY* 3.8 4.5 - - - +
94H ASP* 1.3 73.1 - - - +
96H ALA* 1.3 62.0 + - - +
98H ALA* 3.1 3.6 + - - -
99H ALA* 2.8 27.7 + - - +
108H TYR* 3.7 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H GLY 3.2 15.2 + - - +
93H LYS 3.6 5.2 - - - +
95H LEU* 1.3 80.0 - - - +
97H ASP* 1.3 57.5 + - - +
99H ALA 3.5 0.2 + - - -
100H LYS 3.0 21.5 + - - -
108H TYR* 3.6 16.1 + - - +
137H TYR* 3.9 11.4 - - + -
138H VAL* 4.5 15.7 - - + -
141H LEU* 3.5 21.8 - - + +
143H LEU* 3.5 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H LYS* 2.9 23.6 + - - +
94H ASP* 3.5 13.1 - - - +
96H ALA* 1.3 73.9 - - - +
98H ALA* 1.3 66.0 + - - +
100H LYS* 3.2 5.5 + - - +
101H ARG* 2.9 49.3 + - - +
137H TYR* 2.6 33.2 + - - -
141H LEU* 3.4 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H MET* 3.7 22.0 - - + +
68H ASP* 4.4 5.5 - - - +
71H PHE* 3.3 29.4 - - + +
94H ASP 2.8 13.7 + - - +
95H LEU 3.4 2.9 - - - +
97H ASP* 1.3 75.4 - - - +
99H ALA* 1.3 57.4 + - - +
101H ARG* 3.1 23.6 + - - +
102H ALA* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H PHE* 3.5 22.8 - - + -
95H LEU 2.8 15.3 + - - +
96H ALA 3.7 4.5 - - - +
98H ALA* 1.3 76.7 - - - +
100H LYS* 1.3 62.5 + - - +
102H ALA* 3.2 12.7 + - - +
103H GLY* 3.3 8.7 + - - -
105H ILE* 3.7 18.4 - - + +
108H TYR* 3.6 30.7 - - + -
143H LEU* 4.1 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H ALA 3.0 18.0 + - - +
97H ASP* 3.6 7.0 - - - +
99H ALA* 1.3 75.7 - - - +
101H ARG* 1.3 64.7 + - + +
103H GLY* 3.0 15.8 + - - -
141H LEU* 3.4 50.9 - - + +
143H LEU* 4.3 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H VAL* 4.9 15.2 - - - +
67H MET* 5.7 0.2 - - - +
68H ASP* 3.6 21.1 + - - +
94H ASP* 3.8 4.4 + - - +
97H ASP* 2.9 44.8 + - - +
98H ALA* 3.1 32.0 - - - +
100H LYS* 1.3 77.8 - - + +
102H ALA* 1.3 62.4 + - - +
103H GLY* 3.2 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H ASP 5.9 0.2 - - - +
71H PHE* 3.7 28.5 - - + +
72H GLU* 5.5 1.1 - - - -
98H ALA 2.9 12.2 + - - +
99H ALA* 3.4 10.8 - - - +
100H LYS 3.2 0.2 - - - -
101H ARG* 1.3 76.5 - - - +
103H GLY* 1.3 58.0 + - - +
104H THR* 3.0 31.6 + - - +
105H ILE* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H ALA 3.3 4.0 + - - -
100H LYS* 3.0 16.9 + - - -
101H ARG 3.1 1.5 - - - -
102H ALA* 1.3 77.0 - - - +
104H THR* 1.3 60.8 + - - +
105H ILE 3.6 3.4 - - - +
----------------------------------------------------------
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