Contacts of the helix formed by residues 142 - 156 (chain A) in PDB entry 2P2F
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 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TRP* 3.6 7.6 - - + +
139A MET* 4.0 10.8 - - + -
140A PRO* 2.8 30.0 + - + +
141A MET* 1.3 78.1 - - - +
143A PRO* 1.4 75.9 - - + +
144A GLU* 3.4 18.6 - - - +
145A ALA* 3.1 17.3 + - - +
220A LEU* 3.8 17.7 - - + -
222A ARG* 3.9 31.2 - - - +
329A MET* 3.3 12.3 - - - +
331A GLU* 4.0 8.7 - - - +
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Residues in contact with PRO 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 5.0 10.0 - - + +
97A TRP* 3.6 35.4 - - + +
106A LYS* 4.8 9.4 - - + +
108A ILE* 3.5 31.9 - - + -
113A LEU* 6.2 0.9 - - + -
142A VAL* 1.4 88.4 - - + +
144A GLU* 1.3 70.9 + - - +
146A ALA* 3.0 18.2 + - + +
147A VAL* 3.0 16.6 + - + +
329A MET* 3.7 11.0 - - + -
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Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LYS* 4.6 12.9 + - - -
139A MET* 3.7 17.7 - - + -
142A VAL* 3.1 16.7 + - - +
143A PRO* 1.3 87.3 - - - +
145A ALA* 1.3 59.0 + - - +
147A VAL* 3.6 10.3 - - + -
148A ALA* 2.8 26.3 + - - +
220A LEU* 3.8 26.4 - - + +
237A TRP* 3.4 37.5 - - + +
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Residues in contact with ALA 145 (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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137A ILE* 4.9 4.0 - - + +
139A MET* 3.4 36.2 - - + +
140A PRO 3.9 8.5 - - - +
141A MET* 5.6 0.2 - - - -
142A VAL 3.1 13.8 + - - +
144A GLU* 1.3 77.5 - - - +
146A ALA* 1.3 57.3 + - - +
148A ALA* 3.2 5.0 + - - +
149A MET* 2.9 35.1 + - - +
307A VAL* 4.4 19.7 - - + -
329A MET* 5.3 0.9 - - + -
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 4.0 24.9 - - + -
113A LEU* 5.3 1.1 - - + -
142A VAL 4.1 0.6 + - - -
143A PRO 3.0 11.0 + - - +
145A ALA* 1.3 75.4 - - - +
147A VAL* 1.3 66.2 + - - +
149A MET* 3.9 1.0 - - - +
150A LEU* 2.9 35.4 + - + +
307A VAL* 5.1 0.2 - - - +
317A LEU* 3.8 33.9 - - + -
329A MET* 4.2 9.2 - - + +
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.9 21.8 - - + -
116A ASP* 3.9 32.3 - - + +
117A VAL* 4.0 9.4 - - + +
120A PHE* 3.9 24.2 - - + -
143A PRO* 3.0 20.2 + - + +
144A GLU* 3.2 15.7 + - + +
146A ALA* 1.3 76.1 - - - +
148A ALA* 1.3 56.5 + - - +
150A LEU* 3.9 1.6 - - - +
151A ALA* 3.0 28.4 + - - +
237A TRP* 4.0 13.7 - - + -
241A ILE* 4.8 0.4 - - + -
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Residues in contact with ALA 148 (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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120A PHE* 4.0 14.7 - - + -
137A ILE* 4.0 14.1 - - + -
139A MET* 5.5 0.2 - - + -
144A GLU 2.8 16.8 + - - +
145A ALA* 3.5 11.0 - - - +
147A VAL* 1.3 74.5 - - - +
149A MET* 1.3 61.1 + - - +
151A ALA* 3.3 2.3 + - - +
152A CYS* 3.0 28.4 + - - -
184A ILE* 3.9 29.2 - - + -
237A TRP* 4.2 6.0 - - + -
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Residues in contact with MET 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 3.9 11.2 - - + -
145A ALA* 2.9 22.7 + - - +
146A ALA 3.9 3.4 - - - +
148A ALA* 1.3 71.8 - - - +
150A LEU* 1.3 62.8 + - - +
152A CYS 3.3 1.7 + - - -
153A ALA* 3.1 17.7 + - - +
159A HIS* 3.5 40.9 - - + +
161A VAL* 3.8 19.1 - - + -
307A VAL* 3.5 31.4 - - + -
313A HIS* 3.7 32.5 - - + +
317A LEU* 4.3 12.3 - - + -
318A TYR* 3.4 22.6 + - + +
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Residues in contact with LEU 150 (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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77A LEU* 3.9 14.4 - - + -
78A ALA* 3.7 5.2 - - - +
81A CYS* 4.1 18.2 - - + -
82A LEU* 4.2 16.6 - - + -
113A LEU* 4.3 8.7 - - + -
117A VAL* 3.8 28.9 - - + -
146A ALA* 2.9 26.4 + - + +
149A MET* 1.3 71.9 - - - +
151A ALA* 1.3 60.9 + - - +
153A ALA* 3.2 5.7 + - - +
154A ARG* 2.8 29.1 + - - +
317A LEU* 4.1 8.5 - - + -
318A TYR* 3.7 22.9 - - + -
321A LEU* 4.0 21.8 - - + -
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Residues in contact with ALA 151 (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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117A VAL* 3.7 28.9 - - + +
120A PHE* 3.7 26.9 - - + -
121A ALA* 3.7 8.1 - - - +
124A LEU* 4.0 3.6 - - + -
147A VAL 3.0 18.5 + - - +
148A ALA 3.8 0.4 - - - +
149A MET 3.3 0.2 - - - -
150A LEU* 1.3 72.7 - - - +
152A CYS* 1.3 66.7 + - - +
154A ARG* 3.2 12.2 + - - +
155A ILE* 3.3 20.1 + - - +
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Residues in contact with CYS 152 (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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124A LEU* 3.8 20.2 - - - -
135A VAL* 3.8 35.2 - - - -
137A ILE* 4.3 3.1 - - - -
148A ALA 3.0 18.7 + - - -
149A MET 3.5 8.5 - - - +
151A ALA* 1.3 76.6 - - - +
153A ALA* 1.3 61.4 + - - +
155A ILE* 3.4 1.3 + - - +
156A GLY 3.0 3.5 + - - -
157A ALA* 2.8 41.1 + - + +
159A HIS* 3.8 23.8 - - + -
184A ILE* 5.0 1.1 - - - -
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Residues in contact with ALA 153 (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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76A ASN* 4.2 7.1 + - - +
77A LEU* 3.9 26.2 + - + +
78A ALA* 4.7 1.6 - - - -
149A MET 3.1 13.8 + - - +
150A LEU 3.7 7.6 - - - +
152A CYS* 1.3 75.6 - - - +
154A ARG* 1.3 63.2 + - - +
156A GLY* 3.1 12.1 + - - +
157A ALA 4.4 5.8 - - - -
159A HIS* 4.9 2.4 - - + -
253A MET* 4.6 5.7 - - - +
259A LEU* 3.8 28.8 - - + +
318A TYR* 4.6 4.3 - - - +
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Residues in contact with ARG 154 (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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76A ASN* 2.8 25.3 - - - +
78A ALA* 3.6 26.0 + - + +
79A ALA 4.4 1.2 - - - +
82A LEU* 4.8 3.2 - - - +
83A ASP* 2.6 42.6 + - - -
114A HIS* 3.8 6.1 + - - -
117A VAL* 3.9 17.7 - - - +
118A CYS* 3.7 18.7 - - - -
121A ALA* 4.2 7.2 - - + -
150A LEU 2.8 13.9 + - - +
151A ALA* 3.4 11.9 - - - +
152A CYS 3.2 0.4 - - - -
153A ALA* 1.3 78.4 - - - +
155A ILE* 1.3 60.2 + - + +
248A HIS* 2.8 53.3 + - + +
250A PRO* 3.4 15.8 - - + +
251A GLU 4.5 5.2 + - - -
253A MET* 3.7 6.2 - - - +
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Residues in contact with ILE 155 (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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121A ALA* 3.7 29.6 - - + -
124A LEU* 3.9 33.7 - - + -
125A LEU* 3.8 38.0 - - + +
129A ILE* 4.1 19.5 - - + +
130A LYS 5.3 1.6 - - - +
131A LYS* 3.9 16.5 + - - +
151A ALA 3.5 9.2 - - - +
152A CYS 3.5 7.0 - - - +
154A ARG* 1.3 77.0 - - - +
156A GLY* 1.3 58.9 + - - +
157A ALA* 3.8 7.6 - - + +
248A HIS* 3.9 8.3 - - - +
253A MET* 3.7 11.7 - - - +
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Residues in contact with GLY 156 (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 LYS* 3.7 9.0 - - - +
132A GLY* 3.2 16.3 + - - -
152A CYS 3.0 4.7 + - - -
153A ALA* 3.1 12.1 + - - -
154A ARG 3.3 0.8 + - - -
155A ILE* 1.3 78.6 - - - +
157A ALA* 1.3 66.3 + - - +
158A VAL* 4.3 3.1 - - - +
253A MET* 3.7 21.3 - - - +
258A PRO 4.4 6.4 - - - +
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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
------------------------------------------------------------
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