Contacts of the helix formed by residues 161 - 178 (chain A) in PDB entry 3PL7
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 VAL 161 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO* 4.6 19.7 - - + -
159A MET* 3.9 9.9 - - + +
160A GLN* 1.3 74.6 + - - +
162A LEU* 1.3 63.6 + - - +
163A VAL 3.3 1.2 + - - -
164A SER* 3.4 17.2 + - - -
165A ARG* 3.5 33.9 + - - +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 3.5 32.3 - - + -
115A THR 4.2 3.8 - - - +
116A PRO* 3.9 13.0 - - + +
119A ALA* 3.5 24.7 - - + -
154A SER* 3.4 18.4 - - - +
159A MET* 2.9 29.8 + - + +
161A VAL* 1.3 76.3 - - + +
163A VAL* 1.3 58.1 + - - +
164A SER 3.4 0.2 - - - -
165A ARG* 3.2 31.8 + - - +
166A ILE* 2.8 41.4 + - + +
169A TRP* 4.3 6.1 - - + -
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.2 8.7 - - + -
24A TRP* 3.8 26.9 - - + -
27A PHE* 4.0 24.5 - - + -
151A CYS* 4.0 33.5 - - + +
154A SER* 4.5 3.6 - - - -
155A VAL* 3.8 28.5 - - + -
160A GLN 3.1 13.9 + - - +
162A LEU* 1.3 76.7 - - - +
164A SER* 1.3 59.0 + - - +
166A ILE* 3.5 2.9 + - - +
167A ALA* 3.0 26.7 + - - +
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TRP* 4.9 5.8 - - - -
27A PHE 3.8 19.3 + - - -
28A SER* 5.5 4.0 - - - -
160A GLN 4.7 0.4 + - - -
161A VAL 3.4 11.5 + - - -
163A VAL* 1.3 77.1 - - - +
165A ARG* 1.3 72.2 + - - +
167A ALA* 3.4 7.7 - - - +
168A ALA* 2.9 22.7 + - - +
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Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO* 4.1 22.4 + - - +
161A VAL* 3.5 37.3 + - - +
162A LEU* 3.4 28.8 - - - +
164A SER* 1.3 80.2 + - - +
166A ILE* 1.3 51.0 + - - +
168A ALA* 2.9 9.8 + - - +
169A TRP* 2.8 64.7 + - + +
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Residues in contact with ILE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ILE* 6.4 0.2 - - + -
119A ALA* 6.2 0.7 - - + -
123A PHE* 5.0 1.3 - - + -
147A GLY* 4.0 7.0 - - - +
150A LEU* 3.8 38.8 - - + -
151A CYS* 3.7 19.7 - - - +
154A SER* 3.8 22.4 - - - +
162A LEU* 2.8 30.7 + - + +
163A VAL 3.7 4.0 - - - +
165A ARG* 1.3 69.8 - - - +
167A ALA* 1.3 64.4 + - - +
169A TRP* 3.1 29.0 + - + +
170A MET* 2.9 42.9 + - + +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.5 14.3 - - + +
10A VAL* 5.2 3.6 - - + -
13A LEU* 3.6 24.9 - - + +
24A TRP* 3.7 19.7 - - + -
163A VAL 3.0 14.7 + - - +
164A SER* 3.4 10.1 - - - +
166A ILE* 1.3 77.6 - - - +
168A ALA* 1.3 56.5 + - - +
170A MET* 3.4 0.4 + - - -
171A ALA* 3.0 29.0 + - - +
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Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER 2.9 12.9 + - - +
165A ARG* 2.9 11.7 + - - +
167A ALA* 1.3 72.8 - - - +
169A TRP* 1.3 70.4 + - + +
171A ALA* 3.2 7.9 + - - +
172A THR* 2.9 28.7 + - - +
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Residues in contact with TRP 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO 5.7 0.9 - - - -
119A ALA* 3.6 19.5 - - + -
120A TYR* 3.3 63.2 - + + +
123A PHE* 3.7 37.2 - + + -
150A LEU* 5.6 1.1 - - + -
162A LEU* 4.3 4.7 - - + -
165A ARG* 2.8 45.7 + - + +
166A ILE* 3.1 33.2 + - + +
168A ALA* 1.3 76.0 - - + +
170A MET* 1.3 57.8 + - - +
172A THR* 3.4 5.2 + - - -
173A TYR* 2.9 31.2 + - - +
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Residues in contact with MET 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.1 13.0 - - + -
13A LEU* 4.1 21.8 - - + -
123A PHE* 3.7 20.6 - - + -
143A PHE* 3.8 24.9 - - + +
144A PHE* 3.9 46.0 - - + +
147A GLY* 3.6 24.2 - - - -
166A ILE* 2.9 28.3 + - - +
167A ALA 3.8 3.6 - - - +
169A TRP* 1.3 74.6 - - - +
171A ALA* 1.3 58.9 + - - +
173A TYR 3.7 0.5 - - - -
174A LEU* 2.8 33.2 + - - +
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 5.0 2.5 - - - +
6A ARG* 4.3 29.6 - - + +
9A VAL* 4.1 11.2 - - + +
167A ALA 3.0 18.7 + - - +
168A ALA* 3.5 7.6 - - - +
170A MET* 1.3 78.1 - - - +
172A THR* 1.3 62.7 + - - +
174A LEU* 3.4 4.4 + - - +
175A ASN* 3.1 34.3 + - - +
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Residues in contact with THR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ALA* 2.9 17.6 + - - +
169A TRP* 4.0 4.9 - - - -
171A ALA* 1.3 75.4 - - - +
173A TYR* 1.3 64.9 + - - +
175A ASN* 3.2 7.7 + - - +
176A ASP* 3.0 43.5 + - - +
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Residues in contact with TYR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 4.7 7.9 - + + -
124A GLU* 6.6 0.2 - - + -
127A VAL* 3.1 35.5 + - + +
128A ASN* 3.8 19.5 + - - -
131A PHE* 3.3 34.3 - + - +
143A PHE* 3.9 16.4 - + + -
169A TRP 2.9 18.2 + - - +
170A MET 3.8 3.1 - - - +
172A THR* 1.3 78.4 - - - +
174A LEU* 1.3 57.4 + - - +
177A HIS* 2.9 68.5 + + + +
178A LEU* 3.6 16.7 + - + +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASN* 3.8 45.8 - - + +
8A LEU* 4.9 5.6 - - + -
9A VAL* 4.2 5.8 - - + -
140A ILE* 6.1 0.7 - - + -
143A PHE* 4.5 8.3 - - + -
144A PHE* 4.0 26.9 - - + -
170A MET 2.8 20.2 + - - +
171A ALA 3.5 4.7 - - - +
173A TYR* 1.3 72.2 - - - +
175A ASN* 1.3 60.8 + - - +
178A LEU* 3.2 27.4 + - + -
179A GLU* 2.9 30.2 + - - +
182A ILE* 4.1 19.3 - - + -
188A TRP* 4.6 4.0 - - + -
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Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN 4.4 12.4 + - - +
5A ASN* 2.5 42.0 + - - +
6A ARG* 5.5 1.6 - - - +
171A ALA* 3.1 22.9 + - - +
172A THR* 3.7 7.3 - - + +
174A LEU* 1.3 81.5 - - - +
176A ASP* 1.3 66.2 + - - +
179A GLU* 3.7 12.7 - - - +
180A PRO* 4.0 12.8 - - - +
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Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A THR* 3.0 36.7 + - - +
175A ASN* 1.3 83.7 - - - +
177A HIS* 1.3 84.2 + - + +
178A LEU 3.9 0.2 - - - -
180A PRO* 4.3 11.3 - - - +
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Residues in contact with HIS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASN* 5.8 1.1 + - - -
135A VAL* 4.9 6.4 - - - +
173A TYR* 2.9 59.6 + + + +
176A ASP* 1.3 103.0 + - + +
178A LEU* 1.3 65.0 + - - +
179A GLU 3.9 0.2 - - - -
180A PRO* 4.2 5.7 - - - +
181A TRP* 5.0 3.6 + - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A PHE* 3.7 46.7 - - + -
135A VAL* 4.1 19.1 - - + -
140A ILE* 4.4 11.7 - - + -
143A PHE* 4.0 21.5 - - + -
173A TYR* 3.6 24.7 + - + +
174A LEU* 3.2 24.0 + - + +
177A HIS* 1.3 82.3 - - - +
179A GLU* 1.3 68.8 + - - +
180A PRO* 3.3 3.1 - - - -
181A TRP* 3.0 8.7 + - - +
182A ILE* 2.9 28.3 + - + +
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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) + - + + + + + -
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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