Contacts of the helix formed by residues 158 - 170 (chain A) in PDB entry 3RC3
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 LEU 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A VAL* 4.5 9.9 - - + -
97A LEU* 3.8 29.6 - - + -
100A PHE* 4.0 15.9 - - + -
127A PHE* 4.0 14.6 - - + -
141A ILE* 4.2 25.8 - - + -
144A VAL* 4.4 8.5 - - + -
145A LEU* 3.8 27.4 - - + -
148A ILE* 4.2 10.8 - - + +
155A ALA 3.3 13.6 + - - +
156A ASP 3.0 0.6 - - - -
157A ASP* 1.3 80.2 - - - +
159A PHE* 1.3 64.4 + - - +
160A PRO* 3.4 0.7 - - - -
161A PHE* 3.2 11.5 + - + +
162A PHE* 3.2 17.7 + - - +
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Residues in contact with PHE 159 (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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100A PHE* 3.8 24.9 - + + -
106A ILE* 3.9 17.5 - - + -
109A LEU* 3.8 29.6 - - + -
110A GLY* 3.7 33.7 - - - -
113A TYR* 3.8 30.3 - + - -
115A LEU* 5.3 0.2 - - + -
156A ASP 2.9 18.4 + - - +
158A LEU* 1.3 77.7 - - - +
160A PRO* 1.4 64.1 - - + +
162A PHE* 3.2 18.9 + + - +
163A LEU* 2.9 45.7 + - + -
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Residues in contact with PRO 160 (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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156A ASP 4.1 1.6 - - - +
157A ASP* 3.2 21.1 - - - +
158A LEU 3.4 0.9 - - - -
159A PHE* 1.4 96.1 - - + +
161A PHE* 1.3 59.5 + - + +
163A LEU* 3.8 9.9 - - + +
164A ARG* 3.1 57.4 + - - +
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Residues in contact with PHE 161 (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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127A PHE* 4.0 5.8 - - + -
140A ASP* 3.5 41.5 - - + -
141A ILE* 3.8 36.6 - - + -
144A VAL* 3.9 28.0 - - + -
157A ASP 3.6 25.1 - - - -
158A LEU* 3.2 15.9 + - + +
160A PRO* 1.3 78.4 - - + +
162A PHE* 1.3 67.6 + - - +
164A ARG* 3.3 24.2 + - - +
165A HIS* 2.9 23.0 + - - +
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Residues in contact with PHE 162 (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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100A PHE* 3.6 31.9 - + + -
115A LEU* 3.8 19.1 - - + -
120A PHE* 3.7 46.7 - + - -
123A ALA* 3.7 14.8 - - + -
124A PHE* 3.6 31.6 - - + -
127A PHE* 3.7 36.9 - + + -
158A LEU 3.2 3.6 + - - +
159A PHE* 3.2 21.4 + + - +
161A PHE* 1.3 79.8 - - - +
163A LEU* 1.3 53.6 + - - +
165A HIS* 3.1 4.7 + - + +
166A ALA* 2.8 30.8 + - - +
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Residues in contact with LEU 163 (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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113A TYR* 3.6 59.9 - - + +
115A LEU* 4.5 15.3 - - + -
159A PHE* 2.9 27.4 + - + +
160A PRO* 3.8 7.9 - - + +
162A PHE* 1.3 77.6 - - - +
164A ARG* 1.3 67.5 + - + +
166A ALA* 3.1 6.8 + - + +
167A LYS* 2.9 50.4 + - + +
173A LEU* 5.8 2.2 - - + -
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Residues in contact with ARG 164 (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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140A ASP* 4.1 17.6 + - - -
160A PRO* 3.1 45.0 + - - +
161A PHE* 4.0 22.0 - - - +
163A LEU* 1.3 76.5 - - + +
165A HIS* 1.3 63.5 + - - +
167A LYS* 3.2 25.7 + - - +
168A GLN* 3.1 25.9 + - - +
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Residues in contact with HIS 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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69A VAL* 3.7 31.9 - - + +
123A ALA 3.8 7.4 - - - -
126A SER* 2.9 24.9 + - - -
127A PHE* 3.4 41.7 + + + -
130A TYR* 3.9 27.2 - + + +
161A PHE 2.9 13.1 + - - +
162A PHE 3.3 8.7 - - - +
164A ARG* 1.3 78.5 - - - +
166A ALA* 1.3 62.7 + - - +
168A GLN* 3.2 19.9 + - - +
169A ILE* 3.1 27.7 + - + +
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Residues in contact with ALA 166 (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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115A LEU* 3.9 29.4 - - + -
123A ALA* 3.7 28.9 - - + -
162A PHE* 2.8 13.1 + - + +
163A LEU* 3.1 10.1 + - + +
165A HIS* 1.3 78.1 - - - +
167A LYS* 1.3 58.0 + - - +
169A ILE* 3.2 5.4 + - - +
170A PHE* 2.8 32.8 + - + +
173A LEU* 4.4 4.0 - - + -
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Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A TYR* 6.5 0.2 - - + -
163A LEU* 2.9 40.0 + - + +
164A ARG* 3.7 20.7 - - - +
165A HIS 3.1 0.4 - - - -
166A ALA* 1.3 78.5 - - - +
168A GLN* 1.3 56.6 + - - +
170A PHE 3.9 5.8 - - - -
171A PRO* 3.2 28.9 - - - +
173A LEU* 4.3 19.3 - - + +
174A ASP* 2.6 42.2 + - + +
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Residues in contact with GLN 168 (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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67A LEU* 3.7 21.3 - - - +
69A VAL* 4.1 27.4 - - + +
164A ARG* 3.1 24.4 + - - +
165A HIS* 3.2 24.9 + - - +
167A LYS* 1.3 72.4 - - - +
169A ILE* 1.3 63.9 + - - +
170A PHE 3.2 1.3 - - - -
171A PRO* 3.8 3.7 - - - +
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Residues in contact with ILE 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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65A VAL 4.2 0.9 - - - +
66A PRO* 3.6 23.2 - - + +
67A LEU* 2.9 40.9 + - - +
69A VAL* 3.4 28.7 - - + -
122A GLN 5.2 2.2 - - - +
123A ALA* 4.4 11.7 - - - -
126A SER* 3.4 24.0 - - - +
165A HIS* 3.1 28.9 + - + +
166A ALA* 3.5 10.1 - - - +
168A GLN* 1.3 77.0 - - - +
170A PHE* 1.3 87.1 + - + +
171A PRO* 3.7 3.5 - - - +
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Residues in contact with PHE 170 (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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64A PHE* 3.8 31.6 - - + -
65A VAL 4.7 1.1 - - - -
66A PRO* 3.6 27.4 - - + -
119A LEU* 3.6 48.0 - - + -
122A GLN* 3.6 30.3 - - + -
123A ALA* 4.1 6.1 - - + -
166A ALA 2.8 13.9 + - - +
167A LYS 3.4 5.9 - - - +
169A ILE* 1.3 105.7 - - + +
171A PRO* 1.4 66.2 - - - +
172A VAL 3.1 3.4 - - - -
173A LEU* 3.0 35.4 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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