Contacts of the helix formed by residues 152 - 170 (chain A) in PDB entry 5VS1
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 ARG 152 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE 3.4 1.0 + - - -
151A PRO* 1.3 70.9 - - - +
153A GLU* 1.3 62.6 + - - +
155A MET* 3.1 9.2 + - - +
156A LEU* 3.0 36.0 + - + +
181A PHE* 2.8 67.8 + - + +
182A ARG* 5.2 0.2 - - - +
184A GLY* 3.2 17.9 - - - -
185A ALA 2.7 35.3 + - - +
186A GLU* 3.0 46.6 + - - +
187A SER* 5.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PRO* 3.2 7.8 - - + +
152A ARG* 1.3 76.4 - - - +
154A GLU* 1.3 61.7 - - + +
156A LEU* 3.4 16.7 + - + +
157A GLN* 3.3 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.9 6.5 - - + +
151A PRO* 3.1 32.8 + - + +
153A GLU* 1.3 77.3 - - + +
155A MET* 1.3 60.7 + - - +
157A GLN* 3.1 14.1 + - - +
158A MET* 3.0 35.2 + - - +
241A LEU* 3.7 18.1 - - + +
250A TYR* 3.7 31.6 - - + +
251A PRO* 5.5 0.5 - - - +
253A ARG* 2.6 35.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.5 35.7 - - + +
151A PRO 3.1 16.6 + - - +
152A ARG* 3.1 12.1 + - - +
154A GLU* 1.3 76.7 - - - +
156A LEU* 1.3 57.2 + - - +
158A MET* 3.3 9.1 + - - +
159A GLN* 2.9 31.4 + - - +
177A VAL* 4.2 3.8 - - + -
181A PHE* 3.6 38.3 - - + -
188A SER* 3.7 20.9 - - - +
190A ASP 3.9 9.4 - - - +
191A MET* 3.7 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ARG* 3.0 31.3 + - + +
153A GLU* 3.4 17.5 - - + +
154A GLU 3.2 0.2 - - - -
155A MET* 1.3 78.6 - - - +
157A GLN* 1.3 59.8 + - + +
159A GLN* 3.7 19.4 + - - +
160A ASP* 3.3 21.0 + - - +
181A PHE* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU* 3.5 27.5 - - + +
154A GLU* 3.1 17.5 + - - +
156A LEU* 1.3 77.4 - - + +
158A MET* 1.3 64.3 + - - +
160A ASP* 3.4 7.5 + - - +
161A ILE* 3.2 28.1 + - + +
241A LEU* 3.7 30.5 - - + +
242A PRO* 5.6 2.8 + - - +
250A TYR* 4.2 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 3.9 27.4 - - + -
154A GLU* 3.0 23.3 + - - +
155A MET* 3.3 6.7 + - - +
157A GLN* 1.3 74.7 - - - +
159A GLN* 1.3 64.8 + - - +
160A ASP 3.4 0.2 + - - -
161A ILE* 3.4 2.6 + - - +
162A VAL* 3.0 28.1 + - - +
191A MET* 3.5 31.6 - - + -
223A PHE* 4.0 13.2 - - + -
239A CYS* 3.5 31.4 - - - -
241A LEU* 3.6 25.8 - - + +
253A ARG* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A MET 2.9 16.8 + - - +
156A LEU* 3.8 31.8 + - - +
158A MET* 1.3 75.5 - - - +
160A ASP* 1.3 56.4 + - - +
162A VAL* 3.8 1.3 - - - -
163A LEU* 2.9 53.9 + - + +
177A VAL* 3.6 26.1 + - + +
181A PHE* 3.4 24.3 - - + -
191A MET* 3.2 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU 3.3 12.9 + - - +
157A GLN* 3.7 9.6 - - - +
158A MET 3.3 0.4 - - - -
159A GLN* 1.3 77.4 - - - +
161A ILE* 1.3 73.3 + - - +
163A LEU* 4.0 3.4 - - - +
164A ASN* 3.0 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLN* 3.2 16.4 + - + +
158A MET 3.7 5.4 - - - +
160A ASP* 1.3 83.5 - - - +
162A VAL* 1.3 62.2 + - - +
164A ASN* 3.7 3.1 - - - +
165A GLU* 2.9 49.1 + - + +
218A LEU* 4.6 0.4 - - + -
221A VAL* 4.9 3.4 - - + -
223A PHE* 3.8 36.3 - - + -
241A LEU* 3.7 23.8 - - + -
242A PRO* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MET 3.0 19.2 + - - +
159A GLN* 3.9 4.5 - - - +
161A ILE* 1.3 75.3 - - - +
163A LEU* 1.3 66.1 + - + +
165A GLU* 3.9 1.0 - - - +
166A VAL* 2.9 37.5 + - + +
175A ALA* 4.9 0.4 - - + -
177A VAL* 5.9 0.7 - - + -
191A MET* 4.3 11.4 - - + -
193A VAL* 4.1 28.0 - - + -
218A LEU* 4.3 21.9 - - + +
223A PHE* 3.6 31.4 - - + -
255A ILE* 4.7 2.7 - - + -
257A ILE* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLN* 2.9 44.5 + - + +
160A ASP* 4.1 3.1 - - - +
162A VAL* 1.3 79.3 - - + +
164A ASN* 1.3 61.1 + - - +
166A VAL* 3.2 6.3 + - - +
167A LYS* 2.8 33.5 + - - +
175A ALA* 3.8 40.2 - - + +
177A VAL* 4.7 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP* 3.0 44.8 + - - +
161A ILE* 3.8 4.0 - - - +
163A LEU* 1.3 76.5 - - - +
165A GLU* 1.3 58.6 + - - +
167A LYS* 3.3 27.2 - - - +
168A LYS* 3.0 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 2.9 31.2 + - + +
162A VAL 4.0 0.2 - - - +
164A ASN* 1.3 71.6 - - - +
166A VAL* 1.3 66.0 + - - +
168A LYS* 3.2 39.3 + - - +
169A VAL* 3.3 20.3 + - - +
214A VAL* 6.2 0.4 - - - -
217A GLN* 2.9 34.8 + - + +
218A LEU* 3.7 28.3 - - + -
221A VAL* 3.7 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 2.9 32.0 + - + +
163A LEU* 3.6 5.8 - - - +
165A GLU* 1.3 75.3 - - - +
167A LYS* 1.3 67.0 + - - +
169A VAL* 3.1 19.0 + - - +
170A ASP 3.3 10.4 + - - +
173A TYR* 3.3 38.0 - - + +
175A ALA* 4.6 10.8 - - + +
193A VAL* 6.3 0.2 - - + -
195A LEU* 4.2 14.1 - - + -
214A VAL* 3.5 31.6 - - + -
218A LEU* 5.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 2.8 18.4 + - - +
164A ASN* 3.3 30.5 - - - +
166A VAL* 1.3 72.6 - - - +
168A LYS* 1.3 63.4 + - + +
170A ASP 3.2 16.0 + - - -
171A SER* 3.3 27.2 + - - +
173A TYR 5.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ASN* 3.0 31.4 + - - +
165A GLU* 3.2 40.4 + - - +
166A VAL 3.1 0.6 - - - -
167A LYS* 1.3 77.2 - - + +
169A VAL* 1.3 60.9 + - - +
217A GLN* 4.9 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU 3.3 16.2 - - - +
166A VAL* 3.1 9.5 + - - +
168A LYS* 1.3 78.9 - - - +
170A ASP* 1.3 63.3 + - + +
173A TYR* 3.8 20.2 - - + -
213A GLN* 4.0 38.8 + - + +
214A VAL* 4.8 2.9 - - - -
217A GLN* 3.5 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A VAL 3.3 3.7 + - - +
167A LYS* 3.2 6.8 + - - -
169A VAL* 1.3 85.8 - - + +
171A SER* 1.3 60.6 + - - +
172A GLU* 2.9 32.2 + - - +
173A TYR* 3.1 36.1 + - + +
197A HIS* 2.8 29.9 + - - -
210A LEU* 5.6 0.5 - - - +
213A GLN* 6.0 1.3 - - - +
----------------------------------------------------------
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