Contacts of the helix formed by residues 122 - 135 (chain A) in PDB entry 3RC0
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 TRP 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A SER* 3.3 28.5 + - - +
121A GLY* 1.3 79.6 - - - +
123A VAL* 1.3 61.0 + - - +
124A PRO* 3.3 2.7 - - - -
125A LEU* 3.0 10.6 + - + +
126A LEU* 2.8 37.6 + - + +
217A VAL* 4.1 9.0 - - + -
220A VAL* 3.6 28.9 - - + -
221A MET* 3.6 36.6 - - + -
241A PRO* 3.5 21.1 - - + +
296A MET* 4.6 7.2 - - + -
475A EDO 3.6 26.7 - - - +
307P GLU 2.4 34.4 + - - -
308P THR* 4.1 12.6 - - - -
309P PHE* 5.0 3.1 - + + -
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Residues in contact with VAL 123 (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 LEU* 3.4 15.7 - - + +
118A SER* 3.4 26.7 - - - +
121A GLY 3.5 0.2 - - - -
122A TRP* 1.3 77.1 - - - +
124A PRO* 1.3 70.1 - - + +
126A LEU* 3.1 8.9 + - - +
127A LEU* 2.9 36.8 + - + +
187A GLU* 4.0 20.2 - - + +
191A ILE* 3.9 21.3 - - + -
192A VAL* 3.7 22.9 - - + -
213A TYR* 4.1 4.9 - - - +
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Residues in contact with PRO 124 (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 GLN* 3.7 36.6 - - + +
109A LEU* 3.5 28.2 - - + +
113A ARG* 5.8 4.7 - - + +
116A LEU* 3.9 25.8 - - + +
121A GLY* 3.9 13.0 - - - +
122A TRP 3.5 3.1 - - - -
123A VAL* 1.3 96.1 - - + +
125A LEU* 1.3 61.8 + - - +
127A LEU 3.4 0.3 + - - -
128A ALA* 3.0 18.7 + - - +
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Residues in contact with LEU 125 (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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98A LEU 3.9 22.0 - - - +
99A SER* 4.2 13.2 - - - -
100A GLN* 4.3 8.7 + - - +
122A TRP* 3.0 11.3 + - + +
124A PRO* 1.3 78.3 - - - +
126A LEU* 1.3 59.1 + - - +
128A ALA* 3.2 5.1 + - + +
129A LEU* 2.9 40.2 + - + +
220A VAL* 3.8 27.8 - - + -
240A SER* 4.5 8.3 + - - +
241A PRO* 3.6 45.3 - - + +
243A MET* 4.3 13.5 - - + -
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Residues in contact with LEU 126 (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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122A TRP* 2.8 36.6 + - + +
123A VAL* 3.1 5.6 + - + +
125A LEU* 1.3 77.2 - - - +
127A LEU* 1.3 56.3 + - + +
129A LEU* 3.4 5.7 + - + +
130A LEU* 2.8 36.4 + - + +
213A TYR* 3.3 42.0 - - + +
216A LEU* 3.7 30.1 - - + +
217A VAL* 3.9 14.8 - - + +
220A VAL* 3.6 28.5 - - + -
475A EDO 4.1 4.9 - - - +
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Residues in contact with LEU 127 (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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105A ILE* 4.7 2.0 - - - -
109A LEU* 3.9 19.5 - - + -
116A LEU* 3.7 31.0 - - + -
123A VAL* 2.9 27.0 + - + +
124A PRO 3.8 4.5 - - - +
126A LEU* 1.3 74.2 - - - +
128A ALA* 1.3 59.4 + - - +
130A LEU* 4.1 6.5 - - + -
131A HIS* 2.8 33.1 + - - +
192A VAL* 4.0 28.5 - - + +
195A PHE* 3.8 19.1 - - + -
196A MET* 4.2 7.4 - - + -
203A PHE* 3.5 27.1 - - + -
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Residues in contact with ALA 128 (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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98A LEU* 4.9 2.9 - - + -
99A SER 3.9 11.7 - - - +
100A GLN* 4.1 5.4 - - - -
103A CYS* 3.4 37.5 - - + -
105A ILE* 4.9 0.2 - - - -
109A LEU* 4.1 2.8 - - + +
124A PRO 3.0 13.5 + - - +
125A LEU* 3.2 10.7 + - + +
127A LEU* 1.3 75.3 - - - +
129A LEU* 1.3 58.6 + - - +
131A HIS* 3.7 3.4 - - - +
132A GLU* 2.8 37.4 + - - +
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Residues in contact with LEU 129 (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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98A LEU* 3.7 25.8 - - + -
125A LEU* 2.9 25.5 + - + +
126A LEU* 3.7 10.3 - - + +
128A ALA* 1.3 76.1 - - - +
130A LEU* 1.3 62.3 + - - +
132A GLU* 3.3 2.9 + - - +
133A LEU* 2.9 37.0 + - + +
144A PHE* 4.8 0.9 - - + -
147A TRP* 3.7 28.9 - - + -
216A LEU* 4.5 18.4 - - + +
219A LEU* 5.1 1.3 - - + -
220A VAL* 3.7 30.1 - - + -
243A MET* 3.9 19.3 - - + -
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Residues in contact with LEU 130 (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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126A LEU* 2.8 33.6 + - + +
127A LEU* 3.8 10.3 - - + +
129A LEU* 1.3 74.1 - - - +
131A HIS* 1.3 63.7 + - - +
133A LEU* 3.5 5.2 + - - +
134A GLN* 3.4 19.8 + - - +
192A VAL* 4.0 27.1 - - + -
196A MET* 4.3 7.0 - - + -
203A PHE* 3.9 13.9 - - + -
207A VAL* 3.7 29.3 - - + +
209A SER 5.7 0.4 - - - +
212A LEU* 3.9 15.9 - - + -
213A TYR* 4.2 18.4 - - + -
216A LEU* 3.4 24.9 - - + +
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Residues in contact with HIS 131 (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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103A CYS* 5.8 0.2 - - + -
104A SER* 3.1 27.7 + - - -
105A ILE* 3.8 36.6 - - + +
127A LEU 2.8 21.0 + - - +
128A ALA 3.7 2.2 - - - +
130A LEU* 1.3 74.6 - - - +
132A GLU* 1.3 74.5 + - + +
134A GLN* 2.9 34.3 + - - -
135A ALA* 3.0 14.3 + - + +
201A ASP 5.6 0.2 - - - -
202A LEU* 2.8 46.2 + - + +
203A PHE* 3.5 10.0 - - + -
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Residues in contact with GLU 132 (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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98A LEU* 4.2 18.6 - - + -
103A CYS* 3.6 4.8 - - + +
104A SER* 2.8 42.2 + - - -
128A ALA 2.8 25.0 + - - +
129A LEU* 3.3 2.7 + - - +
131A HIS* 1.3 78.6 - - + +
133A LEU* 1.3 61.8 + - - +
135A ALA* 3.4 12.2 + - - +
138A SER* 2.7 51.0 + - - +
139A ARG* 4.3 2.1 + - - -
140A TRP* 3.8 16.1 - - + -
144A PHE* 3.8 23.5 - - + -
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Residues in contact with LEU 133 (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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129A LEU* 2.9 24.5 + - + +
130A LEU* 3.8 5.6 - - - +
131A HIS 3.1 0.2 - - - -
132A GLU* 1.3 77.2 - - - +
134A GLN* 1.3 58.7 + - - +
135A ALA 4.7 2.3 - - - +
144A PHE* 4.0 27.8 - - + -
147A TRP* 4.1 21.5 - - + -
150A LEU* 5.4 3.1 - - + -
206A ARG* 4.6 4.9 + - - -
207A VAL* 4.9 7.6 - - + +
212A LEU* 5.1 10.5 - - + -
216A LEU* 3.8 37.5 - - + -
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Residues in contact with GLN 134 (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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130A LEU 3.4 11.6 + - - +
131A HIS* 2.9 30.0 + - - +
133A LEU* 1.3 77.6 - - - +
135A ALA* 1.3 78.3 + - - +
136A PRO* 3.4 9.4 - - - +
201A ASP 4.5 4.1 + - - +
202A LEU* 3.2 23.0 + - - +
203A PHE* 3.4 4.0 + - - -
204A SER* 2.7 50.8 + - - +
206A ARG* 3.4 23.3 + - - +
207A VAL* 3.6 17.7 - - + -
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Residues in contact with ALA 135 (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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104A SER* 5.5 0.9 - - - +
131A HIS* 3.0 27.3 + - + +
132A GLU* 3.4 17.7 + - - +
133A LEU 4.7 1.9 - - - +
134A GLN* 1.3 84.9 - - - +
136A PRO* 1.3 73.8 - - + +
137A ALA 3.5 1.7 + - - +
138A SER* 3.6 24.2 + - - +
141A ARG* 5.2 2.9 - - - +
206A ARG* 5.6 0.2 - - - -
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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