Contacts of the helix formed by residues 142 - 156 (chain B) in PDB entry 2P2B
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B TRP* 3.6 7.2 - - + +
139B MET* 3.9 24.7 - - + -
140B PRO* 2.9 28.7 + - + +
141B MET* 1.3 73.2 - - - +
143B PRO* 1.4 71.5 - - + +
144B GLU* 3.4 15.3 - - - +
145B ALA* 3.0 26.2 + - - +
220B LEU* 3.9 7.6 - - + -
222B ARG* 3.9 20.9 - - - +
329B MET* 3.3 10.4 - - - +
331B GLU* 3.5 24.2 - - - +
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Residues in contact with PRO 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 5.1 7.7 - - + +
97B TRP* 3.7 32.3 - - + +
106B LYS* 4.8 11.7 - - - -
108B ILE* 3.6 33.7 - - + -
113B LEU* 5.2 1.3 - - + +
142B VAL* 1.4 88.4 - - + +
144B GLU* 1.3 67.4 + - - +
146B ALA* 2.9 23.8 + - + +
147B VAL* 3.0 17.9 + - + +
329B MET* 3.7 9.6 - - + -
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Residues in contact with GLU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LYS* 5.2 9.4 + - - -
139B MET* 3.8 17.9 - - + -
142B VAL* 3.4 20.8 - - - +
143B PRO* 1.3 81.6 - - - +
145B ALA* 1.3 55.7 + - - +
147B VAL* 3.3 10.9 + - + -
148B ALA* 2.9 29.6 + - - +
220B LEU* 3.6 24.7 - - + +
237B TRP* 3.4 35.8 - - + +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 4.7 3.1 - - + +
139B MET* 3.7 29.6 - - + +
140B PRO 3.5 19.1 - - - +
142B VAL 3.0 14.9 + - - +
144B GLU* 1.3 77.9 - - - +
146B ALA* 1.3 57.5 + - - +
148B ALA* 3.4 3.7 + - - +
149B MET* 3.1 34.5 + - - +
307B VAL* 4.4 17.5 - - + -
329B MET* 4.9 1.8 - - + -
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.9 18.8 - - + -
113B LEU* 5.0 0.9 - - + -
142B VAL 3.9 0.6 + - - -
143B PRO 2.9 11.0 + - - +
145B ALA* 1.3 76.3 - - - +
147B VAL* 1.3 66.0 + - - +
148B ALA 3.2 0.2 - - - -
149B MET* 3.3 1.4 + - - +
150B LEU* 2.9 35.9 + - + +
317B LEU* 3.8 38.4 - - + -
329B MET* 4.4 6.8 - - + +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 4.0 19.1 - - + -
116B ASP* 3.6 44.2 - - + +
117B VAL* 3.9 11.8 - - + +
120B PHE* 3.6 15.9 - - + -
143B PRO* 3.0 16.1 + - + +
144B GLU* 3.6 14.6 - - + +
146B ALA* 1.3 75.1 - - - +
148B ALA* 1.3 57.4 + - - +
150B LEU 3.8 0.2 - - - -
151B ALA* 2.8 32.9 + - - +
237B TRP* 3.9 13.5 - - + -
241B ILE* 4.7 0.2 - - + -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 4.0 15.8 - - + -
137B ILE* 3.8 16.8 - - + -
139B MET* 5.3 0.2 - - + -
144B GLU 2.9 17.5 + - - +
145B ALA* 3.5 8.7 - - - +
146B ALA 3.2 0.2 - - - -
147B VAL* 1.3 77.1 - - - +
149B MET* 1.3 61.6 + - - +
151B ALA* 3.8 1.6 - - - +
152B CYS* 3.2 28.6 + - - -
184B ILE* 4.0 22.7 - - + -
237B TRP* 4.2 6.9 - - + -
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Residues in contact with MET 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 3.7 20.6 - - + -
145B ALA* 3.1 15.9 + - - +
146B ALA* 3.7 4.7 - - - +
148B ALA* 1.3 74.4 - - - +
150B LEU* 1.3 63.5 + - - +
152B CYS* 3.1 7.1 + - - +
153B ALA 3.1 17.8 + - - -
159B HIS* 3.7 31.4 - - + +
161B VAL* 3.9 17.0 - - + -
307B VAL* 3.3 29.4 - - + -
313B HIS* 4.0 24.2 - - + +
317B LEU* 3.6 19.7 - - + -
318B TYR* 3.5 21.6 + - + +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.9 15.9 - - + -
78B ALA* 3.7 7.5 - - - +
81B CYS* 3.7 30.3 - - + -
82B LEU* 4.0 17.7 - - + -
113B LEU* 4.2 9.4 - - + -
117B VAL* 3.7 25.1 - - + -
146B ALA* 2.9 29.7 + - + +
149B MET* 1.3 73.4 - - + +
151B ALA* 1.3 57.5 + - - +
153B ALA* 3.5 5.9 + - - +
154B ARG* 2.9 29.1 + - - +
317B LEU* 5.8 2.2 - - + -
318B TYR* 4.1 11.6 + - + -
321B LEU* 3.9 22.9 - - + -
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL* 3.8 15.2 - - + +
120B PHE* 3.5 27.4 - - + -
121B ALA* 3.7 19.0 - - - +
124B LEU* 4.1 4.6 - - + +
147B VAL 2.8 23.4 + - - +
148B ALA 3.8 0.9 - - - +
150B LEU* 1.3 72.5 - - - +
152B CYS* 1.3 63.8 + - - +
154B ARG* 3.3 12.1 + - - +
155B ILE* 3.4 19.4 + - - +
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Residues in contact with CYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.9 15.7 - - - -
135B VAL* 3.7 39.3 - - - -
137B ILE* 4.4 2.9 - - - -
148B ALA 3.2 14.3 + - - +
149B MET 3.1 9.9 + - - +
151B ALA* 1.3 77.8 - - - +
153B ALA* 1.3 62.0 + - - +
155B ILE* 3.2 4.2 + - - +
156B GLY 3.1 3.5 + - - -
157B ALA* 2.9 42.6 + - + +
159B HIS* 4.0 22.0 - - + -
184B ILE* 5.0 1.1 - - - -
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN* 4.1 9.4 + - - +
77B LEU* 3.7 28.4 + - + +
149B MET 3.1 9.3 + - - +
150B LEU* 3.7 8.5 - - - +
152B CYS* 1.3 78.7 - - - +
154B ARG* 1.3 61.4 + - - +
156B GLY* 3.3 10.5 + - - -
157B ALA 4.2 4.7 + - - -
159B HIS* 4.9 1.9 - - + -
253B MET* 4.6 5.7 - - - +
259B LEU* 3.7 30.4 - - + +
318B TYR* 4.4 3.1 - - - +
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN* 3.0 29.7 - - - +
78B ALA* 3.5 19.7 - - + +
82B LEU* 4.8 1.0 - - - +
83B ASP* 2.7 43.4 + - - -
114B HIS* 3.6 5.9 + - - -
117B VAL* 4.2 14.8 - - - +
118B CYS* 3.5 18.9 - - - -
121B ALA* 4.0 10.5 - - - -
150B LEU 2.9 18.7 + - - +
151B ALA* 3.6 7.2 - - - +
152B CYS 3.3 0.4 - - - -
153B ALA* 1.3 75.7 - - - +
155B ILE* 1.3 60.9 + - + +
156B GLY 3.8 0.2 + - - -
248B HIS* 2.7 58.1 + - + -
250B PRO* 3.5 15.9 - - + +
251B GLU* 4.4 4.9 + - - +
253B MET* 4.0 4.9 - - - +
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ALA* 3.8 17.3 - - + +
124B LEU* 3.8 28.3 - - + -
125B LEU* 3.7 36.5 - - + +
129B ILE* 3.9 32.8 - - + +
130B LYS 4.9 1.8 - - - +
131B LYS* 3.6 19.8 + - - +
151B ALA 3.4 6.0 + - - +
152B CYS* 3.2 11.4 + - - +
154B ARG* 1.3 79.5 - - - +
156B GLY* 1.3 58.9 + - - +
157B ALA* 3.5 8.0 + - + +
248B HIS* 3.8 14.1 - - + +
251B GLU* 6.4 0.9 - - - -
253B MET* 3.7 8.7 - - - +
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Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LYS* 3.6 5.3 - - - +
132B GLY* 2.9 23.7 + - - -
152B CYS 3.1 4.1 + - - -
153B ALA* 3.3 10.1 + - - -
154B ARG 3.4 0.4 - - - -
155B ILE* 1.3 77.8 - - - +
157B ALA* 1.3 65.2 + - - +
158B VAL* 4.1 4.3 - - - +
253B MET* 3.6 24.1 - - - +
257B ASP* 6.5 0.4 - - - -
258B PRO 4.4 7.3 - - - +
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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