Contacts of the helix formed by residues 86 - 104 (chain D) in PDB entry 1VI9
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 SER 86 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL* 5.2 4.0 - - - +
57D PRO* 4.3 3.6 - - - +
84D LEU* 3.2 9.3 + - - +
85D GLY* 1.3 82.5 - - - +
87D ALA* 1.3 63.9 + - - +
88D GLU* 3.4 18.4 + - - +
89D GLN* 3.1 37.7 + - - +
90D GLY 3.4 3.5 + - - -
125D ALA* 4.4 4.5 - - - -
126D PRO 5.5 0.4 - - - -
128D VAL* 3.6 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU* 5.6 0.2 - - - -
86D SER* 1.3 74.5 - - - +
88D GLU* 1.3 65.1 + - - +
90D GLY* 2.9 17.5 + - - +
91D GLU* 2.8 26.5 + - - +
126D PRO 5.0 2.9 + - - +
127D GLY* 3.5 31.9 - - - +
128D VAL* 3.7 7.0 - - - +
131D PHE* 4.3 16.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D PRO* 3.9 16.6 - - + -
86D SER* 3.1 14.3 - - - +
87D ALA* 1.3 89.4 + - - +
89D GLN* 1.4 65.7 + - - +
91D GLU* 3.1 36.0 - - + +
92D HIS* 3.3 15.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D THR* 2.8 46.1 + - - +
54D VAL* 3.3 9.6 - - + +
55D MSE 2.9 19.9 + - - +
57D PRO* 3.8 19.3 - - + +
60D LEU* 3.9 20.1 - - + +
84D LEU* 3.5 7.2 - - + -
85D GLY 2.7 28.5 + - - -
86D SER* 3.1 25.0 + - - +
88D GLU* 1.4 75.5 - - - +
90D GLY* 1.3 62.7 + - - +
92D HIS* 3.1 5.0 + - - +
93D ILE* 2.8 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU* 3.5 22.3 - - - +
86D SER 3.4 4.0 + - - -
87D ALA 2.9 11.3 + - - -
89D GLN* 1.3 79.5 - - - +
91D GLU* 1.3 60.6 + - - -
93D ILE* 2.9 14.5 + - - +
94D LEU 3.0 9.9 + - - -
131D PHE* 3.4 26.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ALA* 2.8 30.5 + - - +
88D GLU* 3.1 36.1 + - + +
90D GLY* 1.3 72.7 - - - +
92D HIS* 1.3 68.4 + - + +
94D LEU* 3.2 17.3 + - + +
95D GLY* 3.3 9.0 + - - -
131D PHE* 3.7 15.4 - - + +
135D HIS* 5.3 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D PRO* 3.2 36.2 - - + +
58D SER* 3.6 18.0 + - - -
60D LEU* 4.8 5.4 - - + -
61D THR* 2.8 29.4 + - + +
88D GLU* 3.3 14.6 + - + +
89D GLN* 3.1 9.4 + - - +
91D GLU* 1.3 78.5 - - + +
93D ILE* 1.4 60.5 + - - +
95D GLY* 3.1 3.6 + - - +
96D ILE* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ILE* 3.9 39.7 - - + -
38D THR* 4.8 0.2 - - + -
60D LEU* 4.4 11.0 - - + -
79D VAL* 4.9 0.4 - - + -
81D SER* 4.1 20.0 - - - -
84D LEU* 3.3 35.9 - - + -
89D GLN 2.8 21.5 + - - +
90D GLY* 2.9 7.8 + - - +
92D HIS* 1.4 76.8 - - - +
94D LEU* 1.3 57.0 + - + +
96D ILE* 3.1 7.2 + - + +
97D VAL* 2.8 37.4 + - + +
109D TYR* 4.1 15.0 - - + +
131D PHE* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLY 3.0 14.7 + - - +
91D GLU* 3.5 10.8 - - - +
92D HIS 3.2 0.6 - - - -
93D ILE* 1.3 79.0 - - - +
95D GLY* 1.3 61.7 + - - +
97D VAL* 3.3 8.2 + - + +
98D ARG* 3.1 20.3 + - - +
109D TYR* 4.2 15.7 - - + +
131D PHE* 3.9 17.5 - - + -
135D HIS* 3.6 38.6 - - + +
136D GLY* 4.7 0.2 - - - -
139D ALA* 3.6 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D THR* 6.5 0.4 - - - -
91D GLU 3.3 7.1 + - - -
92D HIS* 3.1 7.2 + - - -
94D LEU* 1.3 74.3 - - - +
96D ILE* 1.3 65.4 + - - +
98D ARG* 3.0 10.8 + - - +
99D GLN* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 3.8 18.2 - - + -
8D ILE* 3.9 18.4 - - + -
36D LEU* 4.4 1.1 - - + -
60D LEU* 3.8 39.0 - - + +
61D THR* 4.0 7.4 + - - +
64D VAL* 3.6 32.3 - - + -
79D VAL* 4.6 2.7 - - + -
92D HIS 2.9 18.5 + - - +
93D ILE* 3.1 16.6 + - + +
95D GLY* 1.3 75.9 - - - +
97D VAL* 1.3 63.2 + - - +
99D GLN* 3.2 15.2 + - - +
100D VAL* 3.0 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D VAL* 4.0 24.2 - - + -
93D ILE* 2.8 19.8 + - + +
94D LEU* 3.6 11.0 - - + +
96D ILE* 1.3 75.8 - - - +
98D ARG* 1.3 64.9 + - - +
100D VAL* 3.5 1.4 + - - +
101D LYS* 2.9 42.0 + - + +
109D TYR* 3.6 56.1 - - + -
139D ALA* 5.1 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LEU 3.1 12.1 + - - +
95D GLY* 3.0 12.0 + - - +
97D VAL* 1.3 78.1 - - - +
99D GLN* 1.3 63.7 + - - +
101D LYS* 3.0 6.6 + - - +
102D ALA* 2.7 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D THR* 3.9 16.2 + - - +
64D VAL* 3.3 33.2 - - + +
65D GLN* 3.5 29.1 + - - +
68D ALA* 4.6 3.6 - - - +
73D LEU* 3.9 15.6 - - + +
95D GLY 2.9 11.3 + - - +
96D ILE* 3.3 22.5 - - - +
98D ARG* 1.3 78.2 - - - +
100D VAL* 1.3 63.7 + - - +
102D ALA* 3.2 7.7 + - - +
103D ALA* 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 4.2 9.6 - - + -
64D VAL* 4.8 0.7 - - + -
73D LEU* 3.9 30.5 - - + -
76D CYS* 3.8 22.9 - - + +
79D VAL* 3.6 30.3 - - + -
96D ILE* 3.0 18.3 + - + +
97D VAL 3.8 2.2 - - - +
99D GLN* 1.3 78.7 - - - +
101D LYS* 1.3 57.4 + - + +
103D ALA* 3.0 5.5 + - - +
104D ASN* 2.8 26.3 + - - +
107D ALA* 3.5 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D VAL* 2.9 39.0 + - + +
98D ARG* 3.8 5.6 - - - +
100D VAL* 1.3 70.2 - - + +
102D ALA* 1.3 64.3 + - - +
104D ASN 3.5 7.6 - - - +
105D PRO* 3.2 31.2 - - + +
107D ALA* 3.4 26.5 - - + +
108D LYS 4.5 0.9 - - - -
109D TYR* 4.3 5.3 - - - +
139D ALA 4.4 10.3 + - - -
141D ASP* 2.7 36.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ARG* 2.7 28.0 + - + +
99D GLN* 3.4 7.6 - - - +
101D LYS* 1.3 73.8 - - - +
103D ALA* 1.3 62.1 + - - +
105D PRO* 4.6 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU* 3.8 17.3 - - + -
74D HIS* 3.3 40.8 - - + +
99D GLN 3.1 10.7 + - - +
100D VAL 3.0 8.3 + - - +
102D ALA* 1.3 79.4 - - - +
104D ASN* 1.3 56.0 + - - +
105D PRO* 4.1 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU 4.8 0.7 - - - +
74D HIS* 3.5 23.3 + - - +
76D CYS 2.7 30.8 + - - +
77D ASP* 4.0 11.3 + - - +
100D VAL 2.8 11.3 + - - +
101D LYS* 3.3 9.6 - - - +
103D ALA* 1.3 73.3 - - - +
105D PRO* 1.3 64.3 - - - +
106D GLN* 3.2 22.8 + - - +
107D ALA* 2.9 34.6 + - + +
----------------------------------------------------------
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