Contacts of the helix formed by residues 159 - 171 (chain A) in PDB entry 4DF3
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 GLU 159 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 1.3 79.7 - - + +
160A GLN* 1.3 65.0 + - - +
161A ALA 3.2 2.6 + - - -
162A ALA* 3.5 21.7 + - + +
163A ILE* 3.6 14.3 + - - +
196A VAL* 6.2 2.0 - - - +
200A GLU* 3.3 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA* 3.5 4.1 - - + +
154A ASP 3.4 10.2 + - - -
155A VAL* 2.7 44.9 + - + +
156A ALA* 4.7 4.9 - - - +
157A GLN 3.5 15.1 + - - +
158A PRO 3.2 1.6 - - - -
159A GLU* 1.3 76.8 - - - +
161A ALA* 1.4 53.7 + - - +
163A ILE* 3.0 12.9 + - + +
164A VAL* 2.8 38.4 + - + +
180A MET* 3.5 24.9 - - + +
181A ALA 2.8 28.1 + - - -
182A ILE* 4.7 2.8 - - - +
200A GLU* 3.1 7.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
159A GLU 3.2 0.4 - - - -
160A GLN* 1.4 72.2 - - - +
162A ALA* 1.3 56.5 + - - +
164A VAL* 3.2 2.5 + - - +
165A VAL* 2.8 32.7 + - - +
180A MET* 4.0 6.7 - - + -
200A GLU* 2.7 49.6 + - + +
203A THR* 3.7 15.0 - - + -
204A LEU* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLU* 3.5 19.3 + - + +
160A GLN 3.3 0.6 - - - -
161A ALA* 1.3 73.4 - - - +
163A ILE* 1.3 66.4 + - + +
165A VAL* 3.4 4.5 + - - +
166A ARG* 3.1 42.5 + - - +
200A GLU* 5.1 0.2 + - - -
203A THR* 3.6 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.9 9.2 - - + -
135A ALA* 3.4 35.0 - - + +
136A ARG* 3.7 32.5 - - + -
155A VAL* 4.3 19.5 - - + -
157A GLN* 4.8 8.5 - - + -
158A PRO 5.0 1.3 - - - +
159A GLU 3.7 15.3 - - - +
160A GLN* 3.0 15.8 + - + +
162A ALA* 1.3 74.0 - - + +
164A VAL* 1.3 68.1 + - + +
166A ARG* 3.4 12.4 + - - +
167A ASN* 2.9 35.1 + - - +
301A SAM 4.8 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 4.7 8.1 - - + -
151A LEU* 3.7 10.1 - - + +
153A ALA* 3.4 33.0 - - + -
160A GLN* 2.8 22.0 + - + +
161A ALA 3.4 8.3 - - - +
163A ILE* 1.3 73.2 - - - +
165A VAL* 1.4 53.3 + - - +
167A ASN 3.4 0.9 + - - -
168A ALA* 2.8 32.8 + - + +
178A MET* 3.4 34.5 - - + -
180A MET* 3.7 15.5 - - + -
204A LEU* 3.9 12.3 - - + -
209A LEU* 4.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA 2.8 23.2 + - - +
162A ALA* 3.9 6.3 - - - +
163A ILE 3.3 0.2 - - - -
164A VAL* 1.4 72.8 - - - +
166A ARG* 1.3 57.3 + - - +
168A ALA* 3.2 6.2 + - - +
169A ARG* 2.9 64.2 + - + +
203A THR* 3.6 26.0 - - + +
204A LEU* 4.1 15.9 - - + +
207A GLY* 4.0 18.4 - - - +
209A LEU* 4.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 2.8 53.6 + - - +
138A PRO* 3.6 18.4 - - + -
162A ALA* 3.1 35.1 + - - +
163A ILE* 3.6 12.6 - - - +
164A VAL 3.2 0.2 - - - -
165A VAL* 1.3 80.0 - - - +
167A ASN* 1.3 61.9 + - - +
169A ARG* 3.4 8.7 + - - +
170A PHE* 3.2 35.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.7 23.0 - - + +
84A LEU* 3.7 16.0 - - + +
135A ALA 2.9 26.1 + - - -
138A PRO* 3.5 17.1 - - - +
141A TYR* 2.7 24.7 + - - -
151A LEU* 4.1 4.0 - - + -
163A ILE* 2.9 33.3 + - - +
164A VAL 3.8 3.6 - - - +
166A ARG* 1.3 76.0 - - - +
168A ALA* 1.3 65.4 + - - +
170A PHE 3.2 1.6 + - - -
171A PHE* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 3.8 7.8 - - + +
164A VAL* 2.8 24.9 + - + +
165A VAL* 3.2 8.3 + - - +
167A ASN* 1.3 73.2 - - - +
169A ARG* 1.3 64.5 + - + +
172A LEU* 3.0 56.3 + - + +
178A MET* 5.9 0.2 - - + -
209A LEU* 5.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL* 2.9 40.1 + - + +
166A ARG* 3.7 9.0 - - - +
167A ASN 3.2 0.2 - - - -
168A ALA* 1.3 79.0 - - + +
170A PHE* 1.3 61.5 - - + +
206A ASP 4.1 7.3 + - - -
207A GLY* 3.8 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PRO* 3.7 24.7 - - + -
139A GLU* 4.2 21.1 - - + -
142A ARG* 3.7 46.4 - - + +
166A ARG* 3.2 29.0 + - + -
167A ASN 3.2 1.9 + - - +
168A ALA 3.2 0.2 - - - -
169A ARG* 1.3 83.2 - - + +
171A PHE* 1.3 88.0 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.5 18.2 - - + -
138A PRO* 3.8 18.8 - - + -
141A TYR* 3.7 26.5 - + - -
142A ARG* 3.7 35.0 - - + -
145A VAL* 3.4 39.7 - - + -
146A GLU 4.0 6.7 - - - +
147A GLY* 3.4 7.9 - - - -
148A VAL* 2.8 39.5 + - + -
151A LEU* 6.3 0.2 - - + -
167A ASN* 3.0 23.1 + - - +
168A ALA 3.3 0.6 + - - -
170A PHE* 1.3 99.1 - - + +
172A LEU* 1.3 64.3 + - - +
----------------------------------------------------------
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