Contacts of the helix formed by residues 155 - 170 (chain A) in PDB entry 2P6U
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 ARG 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A PRO* 4.1 30.7 + - + +
77A LEU* 3.4 31.7 - - - +
78A ARG* 4.3 11.3 - - - +
122A SER* 5.5 4.7 - - - +
123A GLU* 5.0 5.1 + - - +
149A LEU* 4.1 14.1 - - + +
152A SER* 3.0 21.6 + - - +
154A LYS* 1.3 94.4 - - - +
156A GLY* 1.3 68.4 + - - +
157A ALA 3.0 2.9 + - - -
158A THR* 3.1 20.3 + - - -
159A LEU* 3.6 10.1 + - + +
707A PO4 2.8 48.1 + - - -
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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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149A LEU 3.3 16.2 + - - -
150A LEU* 3.7 17.9 - - - -
152A SER 2.7 20.0 + - - -
155A ARG* 1.3 71.4 - - - +
157A ALA* 1.3 53.6 + - - +
159A LEU* 2.7 30.9 + - - +
160A GLU* 3.1 17.7 + - - +
408A LYS* 5.8 1.1 - - - -
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Residues in contact with ALA 157 (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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152A SER 4.5 1.6 + - - -
154A LYS 5.0 2.7 + - - +
155A ARG 3.0 3.3 + - - +
156A GLY* 1.3 69.7 - - - +
158A THR* 1.3 58.0 + - - +
160A GLU* 3.4 7.3 + - - +
161A ILE* 3.0 34.0 + - - +
408A LYS* 5.3 1.0 - - - +
409A LEU* 3.9 21.1 - - + +
414A HIS* 3.4 43.1 + - + +
418A HIS* 3.8 13.5 - - - +
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Residues in contact with THR 158 (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 SER* 4.3 19.1 - - - +
123A GLU* 4.4 11.8 + - - +
126A ASP* 3.9 21.1 - - + +
154A LYS 4.6 5.7 + - - -
155A ARG* 3.1 12.0 + - - -
156A GLY 3.0 0.2 + - - -
157A ALA* 1.3 75.4 - - - +
159A LEU* 1.3 57.5 + - - +
161A ILE* 3.9 0.4 - - + +
162A LEU* 2.6 39.2 + - - +
418A HIS* 3.9 13.9 + - + -
487A TYR* 3.2 26.2 + - - +
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Residues in contact with LEU 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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74A VAL* 4.7 6.7 - - + -
76A PRO* 6.3 1.8 - - + -
122A SER* 4.0 23.1 - - - +
144A VAL* 3.7 27.1 - - + -
145A ASP 5.2 1.3 - - - +
146A GLU 4.4 5.8 - - - +
147A ILE* 4.3 11.9 - - + +
149A LEU* 4.2 17.7 - - + +
150A LEU* 3.6 34.8 - - + +
155A ARG* 3.6 9.1 + - + +
156A GLY* 2.7 17.0 + - - +
158A THR* 1.3 73.7 - - - +
160A GLU* 1.3 63.3 + - - +
162A LEU* 3.7 5.8 - - + +
163A VAL* 3.0 32.9 + - + +
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Residues in contact with GLU 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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150A LEU* 3.3 25.6 - - + +
156A GLY 3.1 10.3 + - - +
157A ALA* 3.7 5.4 - - - +
159A LEU* 1.3 75.3 - - - +
161A ILE* 1.3 63.9 + - + +
163A VAL* 3.9 1.6 - - - +
164A THR* 2.7 30.4 + - - -
191A TRP* 4.1 11.1 - - - -
407A SER* 2.8 29.9 + - - -
408A LYS 3.7 5.4 + - - -
409A LEU* 3.9 11.7 + - + +
441A THR* 2.8 41.2 - - + +
442A PHE* 3.3 12.0 - - + +
443A PHE* 2.8 13.2 + - - +
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Residues in contact with ILE 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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126A ASP* 5.2 2.7 - - - +
157A ALA 3.0 18.2 + - - +
158A THR 3.9 2.0 - - - +
160A GLU* 1.3 75.3 - - - +
162A LEU* 1.3 57.3 + - - +
164A THR* 3.3 2.8 + - - -
165A LYS* 2.8 59.8 + - + +
409A LEU* 3.8 22.9 - - + -
418A HIS* 3.5 45.3 - - + +
421A SER* 5.7 0.9 - - - +
422A ILE* 4.7 3.1 - - + -
437A PHE* 4.0 21.5 - - + -
438A PHE* 4.3 11.7 - - + -
441A THR* 4.9 3.1 - - - +
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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
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74A VAL* 4.1 15.7 - - + -
122A SER* 3.7 39.9 - - - +
125A ALA* 3.8 15.5 - - + -
126A ASP* 4.3 11.2 + - + +
129A ILE* 3.8 13.7 - - + -
142A LEU* 4.6 9.2 - - + -
144A VAL* 5.6 3.1 - - + -
158A THR 2.6 21.7 + - - +
159A LEU* 3.7 8.3 - - + +
161A ILE* 1.3 72.5 - - - +
163A VAL* 1.3 66.8 + - - +
165A LYS* 3.6 6.2 - - - +
166A MET* 2.9 48.5 + - + +
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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
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142A LEU* 4.4 11.2 - - + -
144A VAL* 4.1 26.9 - - + -
147A ILE* 5.1 3.1 - - + -
159A LEU* 3.0 20.8 + - + +
160A GLU 3.9 3.1 - - - +
162A LEU* 1.3 82.2 - - + +
164A THR* 1.3 65.2 + - - +
166A MET* 3.3 1.2 + - - +
167A ARG* 2.8 49.4 + - + +
175A VAL* 4.6 6.5 - - + -
191A TRP* 3.9 27.4 - - + -
192A LEU* 4.1 15.5 - - + -
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Residues in contact with THR 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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160A GLU 2.7 22.6 + - - -
161A ILE* 3.6 3.3 - - - -
163A VAL* 1.3 78.0 - - - +
165A LYS* 1.3 64.8 + - - +
167A ARG* 2.9 9.7 + - - +
168A ARG* 2.8 31.3 + - + +
191A TRP* 4.4 4.0 - - - -
437A PHE* 3.5 36.3 - - + +
440A ASP* 3.8 38.6 + - + -
441A THR* 4.3 5.8 + - - +
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Residues in contact with LYS 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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126A ASP* 2.7 29.5 + - - +
129A ILE* 3.9 13.0 - - + -
130A ARG* 3.7 4.4 - - - +
161A ILE* 2.8 39.5 + - + +
162A LEU* 3.6 4.5 - - - +
164A THR* 1.3 72.3 - - - +
166A MET* 1.3 62.1 + - - +
168A ARG* 3.4 1.2 + - - +
169A MET* 3.0 27.6 + - - +
421A SER* 2.8 27.3 + - - +
422A ILE* 5.3 2.9 - - + +
425A ASP* 3.4 12.3 + - - -
427A TYR* 3.5 47.1 - - + +
437A PHE* 3.5 21.8 - - + -
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Residues in contact with MET 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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72A LEU* 4.3 11.2 - - + -
129A ILE* 4.0 13.7 - - + -
136A ILE* 4.3 24.9 - - + +
139A VAL* 4.5 22.7 - - + +
142A LEU* 3.9 27.8 - - + -
162A LEU* 2.9 37.7 + - + +
163A VAL 3.6 3.8 - - - +
165A LYS* 1.3 74.9 - - - +
167A ARG* 1.3 66.2 + - - +
169A MET* 3.2 11.6 + - + +
170A ASN* 3.0 22.2 + - + +
173A LEU* 3.8 28.0 - - + +
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Residues in contact with ARG 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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42A ASN* 3.7 15.6 - - - +
163A VAL* 2.8 50.9 + - + +
164A THR* 3.5 5.4 - - - +
166A MET* 1.3 71.8 - - - +
168A ARG* 1.3 66.4 + - + +
169A MET 2.9 1.6 + - - -
170A ASN 3.0 26.7 + - - +
171A LYS* 3.8 17.4 + - - +
173A LEU* 4.2 6.8 + - + -
175A VAL* 4.1 20.3 - - + +
191A TRP* 3.3 27.2 + - - +
192A LEU* 3.4 18.1 + - - +
193A ASP* 3.3 22.2 + - - +
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Residues in contact with ARG 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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164A THR* 2.8 28.1 + - + +
165A LYS* 3.8 7.0 - - - +
167A ARG* 1.3 73.4 - - + +
169A MET* 1.3 60.5 + - - +
171A LYS 5.4 0.3 + - - -
427A TYR* 4.6 20.8 + - + +
433A GLU* 4.6 7.9 + - - +
436A ASP* 3.2 16.4 + - - +
437A PHE* 3.0 56.2 - - - +
440A ASP* 3.0 30.4 + - - +
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Residues in contact with MET 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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129A ILE* 4.4 12.3 - - - -
136A ILE* 3.6 28.7 - - + -
137A LYS* 4.0 24.2 - - + -
165A LYS 3.0 16.1 + - - +
166A MET* 3.4 15.5 - - + +
167A ARG 3.0 0.8 - - - -
168A ARG* 1.3 80.5 - - - +
170A ASN* 1.3 60.7 + - + +
171A LYS 4.1 1.0 + - - -
427A TYR* 3.1 32.5 - - + +
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Residues in contact with ASN 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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137A LYS 5.6 4.4 - - - +
139A VAL 4.0 15.1 - - - +
140A SER* 4.7 3.5 - - - -
166A MET* 3.0 11.3 + - + +
167A ARG* 3.1 13.1 - - - +
169A MET* 1.3 80.9 - - + +
171A LYS* 1.3 64.1 - - - +
172A ALA* 3.0 24.7 - - - +
173A LEU* 3.0 42.1 + - + +
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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