Contacts of the helix formed by residues 151 - 166 (chain A) in PDB entry 3FZL
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 151 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY 4.8 2.4 + - - -
76A ARG* 6.2 0.4 - - - +
149A TYR 3.4 3.4 + - - +
150A PHE* 1.3 71.3 - - - +
152A ASP* 1.3 62.3 + - - +
153A SER* 2.6 35.0 + - - -
154A GLN* 2.8 38.9 + - - +
155A ARG* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASN* 1.3 74.1 - - - +
153A SER* 1.3 56.2 + - - +
155A ARG* 3.1 11.0 + - - +
156A GLN* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY* 2.4 31.4 + - - -
151A ASN* 2.6 18.0 + - - -
152A ASP* 1.3 74.8 - - - +
154A GLN* 1.3 50.8 + - - -
156A GLN* 3.2 7.4 + - - +
157A ALA* 2.8 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 3.2 21.1 - - - +
75A GLY* 3.7 17.3 - - - +
76A ARG* 3.4 38.5 + - - +
149A TYR* 4.4 2.4 + - - -
150A PHE* 3.6 37.8 - - + +
151A ASN* 2.8 57.9 + - - +
153A SER* 1.3 69.2 - - - +
155A ARG* 1.3 64.4 + - - +
157A ALA* 4.1 1.4 - - - +
158A THR* 3.0 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 3.5 24.6 - - + +
147A PRO 3.7 1.6 + - - -
148A ALA 3.0 24.9 + - - -
150A PHE* 2.7 32.1 + - + +
151A ASN 2.9 21.4 + - - +
152A ASP* 3.5 9.9 - - - +
154A GLN* 1.3 76.0 - - - +
156A GLN* 1.3 57.0 + - - +
158A THR* 3.3 6.0 + - - -
159A LYS* 2.9 30.8 + - - +
172A ILE* 4.5 22.8 + - + +
174A ASN* 2.8 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ASP 2.8 20.2 + - - +
153A SER* 3.6 6.7 - - - +
155A ARG* 1.3 71.0 - - - +
157A ALA* 1.3 57.4 + - - +
159A LYS* 3.3 23.2 + - - +
160A ASP* 2.7 68.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 3.7 11.2 - - + -
75A GLY* 3.6 26.9 - - - +
117A GLU* 3.2 29.1 - - - +
153A SER 2.8 20.1 + - - +
154A GLN 4.1 1.6 - - - +
156A GLN* 1.3 73.0 - - - +
158A THR* 1.3 56.9 + - - +
160A ASP* 3.9 6.9 - - - +
161A ALA* 2.9 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.2 16.2 - - + +
74A ILE* 3.6 21.7 - - - +
124A LEU* 4.7 1.8 - - + +
144A VAL* 4.0 18.3 - - + +
145A THR 4.8 0.2 - - - +
146A VAL* 3.7 28.7 - - + +
150A PHE* 4.3 1.9 - - - -
154A GLN 3.0 19.3 + - - -
155A ARG 3.3 3.3 + - - -
157A ALA* 1.3 72.3 - - - +
159A LYS* 1.3 67.4 + - - +
161A ALA* 2.9 14.6 + - - +
162A GLY* 3.0 10.4 + - - -
169A VAL* 5.5 0.2 - - - +
172A ILE* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ARG 2.9 20.9 + - - +
156A GLN* 3.7 23.1 - - - +
158A THR* 1.3 72.0 - - - +
160A ASP* 1.3 62.4 + - - +
162A GLY* 3.1 4.7 + - - -
163A THR* 3.0 29.6 + - - +
169A VAL* 3.5 39.7 + - + +
170A LEU 5.1 3.8 + - - -
171A ARG* 5.2 4.8 - - - +
172A ILE* 4.1 24.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
117A GLU* 5.0 8.5 - - + +
156A GLN* 2.7 63.8 + - - +
157A ALA* 3.9 7.2 + - - +
159A LYS* 1.3 68.2 - - - +
161A ALA* 1.3 67.4 + - - +
162A GLY 2.7 3.5 + - - -
163A THR* 2.8 10.4 + - - +
164A ILE* 2.8 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.6 0.2 - - + -
74A ILE* 4.5 0.2 - - + -
117A GLU* 3.4 32.2 - - + +
120A SER* 4.0 17.5 - - - -
121A SER* 3.1 27.5 - - - +
124A LEU* 4.0 7.2 - - + +
157A ALA 2.9 18.8 + - - +
158A THR* 2.9 15.2 + - - +
160A ASP* 1.3 74.3 - - - +
162A GLY* 1.3 58.6 + - - +
164A ILE* 4.7 1.8 - - - -
165A ALA* 3.4 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.8 15.4 - - - +
144A VAL* 5.8 0.7 - - - -
158A THR 3.0 10.2 + - - -
159A LYS 3.1 3.8 + - - -
160A ASP 2.7 4.8 + - - -
161A ALA* 1.3 71.8 - - - +
163A THR* 1.3 55.9 + - - -
164A ILE 3.2 1.6 - - - -
165A ALA* 2.7 24.7 + - - +
167A LEU* 3.1 27.2 + - - +
169A VAL* 4.3 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LYS* 3.0 22.5 + - - +
160A ASP* 2.8 16.6 + - - -
162A GLY* 1.3 69.0 - - - +
164A ILE* 1.3 60.8 + - - +
166A GLY* 3.4 11.4 + - - -
167A LEU 3.7 15.0 + - - +
169A VAL* 4.3 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 4.6 26.7 - - + +
118A GLU* 4.9 11.9 - - + -
121A SER* 3.8 16.8 - - - +
160A ASP* 2.8 31.0 + - + +
161A ALA* 3.9 4.9 - - - +
163A THR* 1.3 74.9 - - - +
165A ALA* 1.3 59.9 + - - +
166A GLY* 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A SER* 3.7 21.8 - - - +
124A LEU* 4.1 8.7 - - + -
125A THR* 3.8 28.4 + - - +
128A LYS* 3.9 14.4 + - - +
161A ALA 3.4 7.7 + - - +
162A GLY* 2.7 19.7 + - - +
164A ILE* 1.3 73.9 - - - +
166A GLY* 1.3 56.0 + - - -
167A LEU* 4.3 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS* 3.9 13.3 - - - -
140A THR* 3.1 24.6 - - - +
162A GLY 3.2 0.8 + - - -
163A THR 3.4 6.3 + - - -
164A ILE 3.2 5.8 - - - -
165A ALA* 1.3 77.8 - - - +
167A LEU* 1.3 63.1 + - - +
----------------------------------------------------------
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