Contacts of the helix formed by residues 144 - 156 (chain A) in PDB entry 5NVN
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 ALA 144 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 3.9 11.9 - - + -
105A GLY* 4.5 8.4 - - - +
139A LEU* 4.3 10.6 - - + +
140A ARG 4.8 0.4 + - - -
142A GLY 3.6 1.4 - - - -
143A LEU* 1.3 78.2 - - - +
145A SER* 1.3 57.9 + - - +
147A CYS* 4.1 0.4 - - - +
148A TRP* 2.8 34.0 + - - +
171A VAL* 4.3 15.8 - - + +
173A VAL* 5.2 0.4 - - + -
178A ASP* 3.2 36.9 + - + +
180A ILE* 4.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 4.4 2.3 + - - -
103A ARG* 3.4 37.6 + - - +
104A PRO* 3.7 10.8 - - - +
105A GLY* 2.7 33.3 + - - +
106A ASP* 4.2 1.4 + - - -
142A GLY 5.1 2.8 + - - -
143A LEU 3.4 0.6 - - - -
144A ALA* 1.3 78.9 - - - +
146A ARG* 1.3 62.5 + - - +
148A TRP* 3.9 1.9 - - - +
149A GLU* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG* 4.1 9.8 - - - +
142A GLY 5.5 1.5 + - - +
143A LEU* 3.6 20.0 + - - +
144A ALA 3.4 0.2 - - - -
145A SER* 1.3 78.8 - - - +
147A CYS* 1.3 70.5 + - - +
149A GLU* 3.3 4.8 + - - +
150A ASN* 3.0 38.9 + - - +
205A ASN* 2.6 52.2 + - - +
206A LEU* 5.8 3.0 - - - +
56B ARG* 5.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 3.6 19.7 - - + -
143A LEU* 3.1 31.0 + - - +
144A ALA 4.1 1.1 - - - +
146A ARG* 1.3 85.0 - - - +
148A TRP* 1.3 57.6 + - - +
150A ASN* 3.2 3.6 + - - +
151A LEU* 2.8 32.5 + - - +
180A ILE* 3.7 22.9 - - + -
204A LEU* 3.7 13.2 - - + +
205A ASN 5.9 1.3 - - - -
206A LEU* 3.8 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 4.2 11.5 - + - -
98A TYR* 4.3 13.6 - + - -
101A MET* 5.8 0.8 - - - +
104A PRO* 3.8 27.4 - - + -
113A PHE* 4.0 30.5 - + + -
115A LEU* 4.1 15.0 - - + -
144A ALA 2.8 20.3 + - - +
145A SER 3.9 1.1 - - - +
147A CYS* 1.3 74.9 - - - +
149A GLU* 1.3 64.8 + - - +
151A LEU* 3.7 8.4 - - + +
152A ILE* 3.1 62.3 + - + +
169A ALA* 3.4 29.2 - - + -
170A VAL 3.4 29.8 - - - -
171A VAL* 3.4 26.1 - - + +
180A ILE* 4.7 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 6.3 0.2 - - + -
95A TRP* 5.1 2.9 - - + -
98A TYR* 2.9 43.2 + - + +
103A ARG* 3.6 17.1 + - - +
145A SER 3.1 13.2 + - - +
146A ARG* 3.6 6.8 - - - +
147A CYS 3.2 0.2 - - - -
148A TRP* 1.3 79.9 - - - +
150A ASN* 1.3 63.4 + - - +
152A ILE* 3.3 8.1 - - + +
153A LEU* 3.0 45.9 + - + +
56B ARG* 3.3 22.4 + - - +
60B MET* 4.1 14.8 - - - +
63B ARG* 4.8 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG* 3.0 41.0 + - - +
147A CYS* 3.8 5.5 - - - +
149A GLU* 1.3 75.2 - - - +
151A LEU* 1.3 63.3 + - - +
153A LEU* 3.9 5.3 - - - +
154A ALA* 3.0 24.6 + - - +
203A VAL* 3.6 23.3 + - - +
204A LEU* 4.0 9.4 - - + +
205A ASN* 3.6 20.2 + - - +
56B ARG* 2.5 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A CYS 2.8 18.3 + - - +
148A TRP* 3.7 14.4 - - + +
150A ASN* 1.3 77.8 - - - +
152A ILE* 1.3 59.6 + - - +
154A ALA* 3.1 6.6 + - - +
155A MET* 2.8 24.9 + - - +
160A PHE* 3.8 16.2 - - + -
169A ALA* 3.7 18.4 - - + -
180A ILE* 4.6 18.2 - - + -
181A SER 3.7 27.1 - - - +
182A ILE* 4.1 9.9 - - + -
200A LEU* 3.6 30.1 - - + -
203A VAL* 5.3 0.7 - - + -
204A LEU* 3.9 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 4.5 5.4 - - + -
94A PHE* 3.8 30.3 - - + -
98A TYR* 3.8 23.8 - - + -
115A LEU* 3.7 18.4 - - + -
148A TRP* 3.1 62.1 + - + +
149A GLU* 3.3 6.7 - - - +
151A LEU* 1.3 72.0 - - - +
153A LEU* 1.3 64.2 + - + +
155A MET* 4.2 7.0 - - + -
156A LEU* 2.7 37.7 + - + +
169A ALA* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 3.6 31.0 - - + -
95A TRP* 3.7 14.8 - - + -
149A GLU* 3.0 36.3 + - + +
150A ASN* 4.0 3.8 - - - +
152A ILE* 1.3 79.4 - - + +
154A ALA* 1.3 56.1 + - - +
156A LEU* 4.7 2.2 - - + -
157A GLY* 3.0 22.9 + - - -
159A GLN* 4.9 0.2 - - - +
54B TYR 4.7 1.4 - - - +
56B ARG* 4.2 29.7 - - + +
59B LEU* 3.3 31.5 - - + +
60B MET* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ASN 3.0 19.6 + - - +
151A LEU 3.4 4.0 - - - +
153A LEU* 1.3 75.0 - - - +
155A MET* 1.3 62.5 + - - +
157A GLY 3.5 0.5 + - - -
158A GLU 3.3 2.9 + - - -
159A GLN* 2.9 41.5 + - + +
160A PHE* 3.9 9.9 - - + -
203A VAL* 3.7 36.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
60A TYR* 3.7 28.5 + - + +
115A LEU* 3.3 46.7 - - + +
151A LEU* 2.8 19.2 + - + +
152A ILE* 3.7 5.4 - - + +
154A ALA* 1.3 72.8 - - - +
156A LEU* 1.3 62.8 + - + +
158A GLU* 3.1 17.2 + - - +
160A PHE* 3.6 16.2 - - + -
166A ILE* 3.9 22.0 - - + -
168A GLY* 3.7 28.3 - - - -
169A ALA* 3.7 17.9 - - + -
182A ILE* 4.4 5.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
56A LEU* 3.9 30.6 - - + +
57A GLN 4.9 2.6 + - - -
60A TYR* 3.2 50.6 + - + -
88A PHE* 4.1 12.1 - - + -
94A PHE* 3.3 51.8 - - + -
115A LEU* 4.3 9.0 - - + -
152A ILE 2.7 24.6 + - - +
153A LEU* 4.2 4.5 - - + +
155A MET* 1.3 73.5 - - + +
157A GLY* 1.3 56.4 + - - +
158A GLU* 3.2 12.4 + - - +
52B ILE 4.9 0.7 - - - +
54B TYR* 4.5 2.8 - - - -
59B LEU* 5.0 5.8 - - + -
----------------------------------------------------------
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