Contacts of the helix formed by residues 147 - 164 (chain J) in PDB entry 1VYH
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 ASN 147 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I GLY 4.0 9.6 - - - +
21I ASP* 3.3 32.8 - - - +
142J ARG 3.2 18.8 + - - +
143J GLY* 4.1 0.9 - - - -
145J LYS 2.9 19.9 - - - +
146J PRO* 1.3 76.7 - - - +
148J PRO* 1.3 76.4 - - + +
149J LEU* 3.0 34.2 + - - +
150J ARG* 3.1 21.3 + - - +
151J GLN* 3.5 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 148 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I GLY* 4.3 14.6 - - - +
147J ASN* 1.3 88.0 - - + +
149J LEU* 1.3 68.9 + - + +
151J GLN* 3.4 14.0 - - + +
152J LYS* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I GLN 3.4 23.8 - - - +
20I GLY* 4.7 1.1 - - - -
21I ASP* 4.0 11.2 - - + +
104J THR 5.2 1.1 - - - +
107J HIS* 3.9 20.9 - - + -
142J ARG* 3.6 42.0 - - - +
147J ASN* 3.0 16.4 + - - +
148J PRO* 1.3 85.5 - - + +
150J ARG* 1.3 67.2 + - - +
151J GLN 3.0 1.8 - - - -
152J LYS* 2.9 37.1 + - + +
153J ASN* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J PRO* 4.1 22.0 - - + +
142J ARG* 3.1 37.9 + - - +
143J GLY 3.2 5.0 + - - -
144J GLU 2.7 32.1 + - - -
145J LYS 3.1 11.3 - - - -
146J PRO* 3.3 27.3 - - + +
147J ASN* 3.1 18.4 + - - +
149J LEU* 1.3 75.9 - - - +
151J GLN* 1.3 63.7 + - - +
153J ASN* 4.0 2.6 + - - +
154J ALA* 3.3 22.0 + - - +
180J VAL* 3.4 20.7 - - - +
184J GLY* 2.7 25.0 + - - -
186J ILE* 4.1 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 151 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J PRO* 5.3 5.5 - - - +
147J ASN 3.5 25.3 + - - +
148J PRO* 3.4 14.4 - - + +
149J LEU 3.0 0.6 - - - -
150J ARG* 1.3 81.3 - - - +
152J LYS* 1.3 64.6 + - - +
154J ALA* 3.2 8.2 - - + +
155J LYS* 3.0 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J GLY 5.9 1.1 - - - -
106J ASN* 3.9 10.5 - - - -
107J HIS* 3.8 24.6 - - - +
108J GLU 4.6 1.4 - - - +
109J ASN 3.5 26.4 + - - +
110J THR* 4.8 1.1 - - - -
111J ALA* 3.7 26.0 - - + +
114J VAL* 5.8 3.8 - - - -
148J PRO 3.0 13.6 + - - +
149J LEU* 2.9 32.3 + - + +
151J GLN* 1.3 75.0 - - - +
153J ASN* 1.3 73.4 + - - +
155J LYS* 2.9 19.5 + - - +
156J VAL* 3.1 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 153 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J GLY 5.1 0.3 - - - +
104J THR* 3.0 30.2 + - - +
139J LEU* 3.3 38.5 - - + +
140J LEU 2.9 28.0 + - - +
141J PRO* 5.0 0.4 - - + +
142J ARG* 3.8 13.3 - - - +
149J LEU* 3.0 17.6 + - - +
150J ARG* 4.3 4.0 - - - +
152J LYS* 1.3 85.3 - - - +
154J ALA* 1.3 63.6 + - - +
156J VAL* 3.1 5.2 + - - +
157J ASN* 3.0 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150J ARG 3.3 15.9 + - - +
151J GLN* 3.2 14.1 + - + +
153J ASN* 1.3 77.3 - - - +
155J LYS* 1.3 63.6 + - - +
157J ASN* 3.1 14.5 + - - +
158J GLN* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 155 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J ALA* 3.7 12.2 - - + +
112J GLU* 4.3 21.8 - - - +
151J GLN* 3.0 29.9 + - - +
152J LYS* 2.9 12.2 + - - +
154J ALA* 1.3 73.6 - - - +
156J VAL* 1.3 64.8 + - - +
158J GLN* 2.8 28.0 + - + +
159J LEU* 2.9 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J ALA* 3.9 15.7 - - + +
114J VAL* 3.2 37.7 - - + -
115J ALA* 4.5 3.8 - - - -
118J ILE* 4.4 5.4 - - + -
139J LEU* 3.7 27.1 - - + -
152J LYS* 3.1 19.1 + - + +
153J ASN* 3.1 6.7 + - - +
155J LYS* 1.3 76.1 - - - +
157J ASN* 1.3 65.4 + - - +
159J LEU* 3.1 6.9 + - - +
160J LEU* 2.9 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 157 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J GLY* 3.0 13.4 - - - -
139J LEU* 2.9 46.7 + - - +
153J ASN* 3.0 20.1 + - - +
154J ALA* 3.4 9.7 - - - +
156J VAL* 1.3 79.6 - - - +
158J GLN* 1.3 63.6 + - - +
160J LEU* 3.3 8.0 + - - +
161J LYS* 3.0 24.8 + - - +
172J LEU* 3.9 6.8 - - + +
174J ASP* 5.1 20.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 158 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J ALA* 3.0 13.9 + - - +
155J LYS* 2.8 28.0 + - + +
157J ASN* 1.3 73.9 - - - +
159J LEU* 1.3 71.3 + - + +
161J LYS* 3.1 13.1 + - - +
162J VAL* 3.4 19.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J ALA* 5.3 0.7 - - + +
112J GLU* 3.8 47.3 - - + +
115J ALA* 3.8 20.2 - - + -
119J GLU* 4.9 2.5 - - - +
155J LYS* 2.9 27.7 + - + +
156J VAL* 3.6 7.0 - - - +
158J GLN* 1.3 85.1 - - + +
160J LEU* 1.3 59.2 + - - +
162J VAL* 3.3 8.4 + - + +
163J SER* 2.9 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J ALA* 4.0 18.8 - - + +
118J ILE* 3.7 37.5 - - + -
119J GLU* 3.6 24.5 - - + +
136J VAL* 4.1 14.1 - - + -
137J LEU 5.8 0.4 - - - +
138J GLY* 5.9 0.9 - - - -
139J LEU* 6.2 0.4 - - + -
156J VAL* 2.9 26.1 + - + +
157J ASN* 3.7 7.9 - - - +
159J LEU* 1.3 74.3 - - - +
161J LYS* 1.3 66.1 + - - +
162J VAL 3.0 2.0 - - - -
163J SER* 4.0 4.3 - - - +
164J LEU* 2.9 45.9 + - + +
172J LEU* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157J ASN 3.0 13.4 + - - +
158J GLN* 3.1 9.4 + - - +
160J LEU* 1.3 76.2 - - - +
162J VAL* 1.3 58.5 + - + +
165J PRO* 3.0 23.8 - - - +
172J LEU* 3.5 20.5 - - + +
174J ASP* 5.9 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158J GLN* 3.6 16.2 - - + +
159J LEU* 3.3 9.8 + - + +
160J LEU 3.0 0.4 - - - -
161J LYS* 1.3 80.8 - - + +
163J SER* 1.3 62.9 + - - +
164J LEU 3.5 0.2 - - - -
165J PRO* 3.4 13.9 - - - +
166J LYS* 4.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 163 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J GLU* 2.7 39.7 + - - +
159J LEU 2.9 15.9 + - - -
160J LEU* 4.0 5.2 - - - +
162J VAL* 1.3 78.8 - - - +
164J LEU* 1.3 63.0 + - - +
165J PRO* 3.6 0.2 - - - -
166J LYS* 3.7 14.3 + - - +
167J LEU* 3.3 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J ILE* 4.9 1.3 - - + -
119J GLU* 4.4 14.6 - - + -
122J VAL* 4.4 22.2 - - + -
136J VAL* 4.0 26.9 - - + -
160J LEU* 2.9 37.1 + - + +
163J SER* 1.3 84.3 - - - +
165J PRO* 1.3 57.6 - - + +
166J LYS 2.3 25.4 - - - +
167J LEU* 3.7 10.3 - - + +
170J VAL* 3.9 25.7 - - + +
171J GLN* 5.3 0.7 - - - -
172J LEU* 3.9 32.3 - - + +
----------------------------------------------------------
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