Contacts of the helix formed by residues 160 - 174 (chain B) in PDB entry 2AFW
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 SER 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ARG* 3.7 6.9 - - - +
139B CYS* 4.6 0.7 - - - -
140B HIS* 3.3 37.8 + - - -
156B GLY 3.3 0.4 + - - -
158B THR 3.4 6.7 + - - -
159B ASP* 1.3 72.0 + - - +
161B ALA* 1.3 65.0 + - - +
162B VAL 3.2 2.7 - - - -
163B PRO* 3.3 15.6 - - - +
164B CYS* 3.1 24.2 + - - -
248B ASP* 2.7 29.8 + - - -
249B LEU 3.6 2.3 + - - -
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.8 8.6 - - + +
73B LEU* 4.1 13.3 - - + +
74B LEU* 3.8 24.0 - - + -
77B ARG* 3.5 18.7 - - - +
156B GLY 3.1 13.0 + - - +
157B ALA 3.3 8.7 + - - +
160B SER* 1.3 77.7 - - - +
162B VAL* 1.3 63.2 + - - +
164B CYS* 3.2 10.7 + - - +
165B ALA* 3.0 22.7 + - - +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B MET* 5.4 0.9 - - + -
70B LEU* 3.9 15.7 - - + -
157B ALA 2.9 18.3 + - - +
161B ALA* 1.3 73.2 - - - +
163B PRO* 1.3 66.9 - - - +
165B ALA* 3.0 4.1 + - - +
166B MET* 2.8 46.7 + - + +
250B ILE 3.2 25.6 - - - +
339B LEU* 3.5 36.1 - - + -
344B ILE* 3.8 25.4 - - + -
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Residues in contact with PRO 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B CYS* 3.7 23.3 - - + -
158B THR 3.5 13.9 - - - +
160B SER* 3.3 26.2 - - - +
162B VAL* 1.3 93.3 - - + +
164B CYS* 1.3 63.2 + - - +
166B MET* 3.2 6.6 + - - +
167B MET* 3.0 27.9 + - - +
247B LEU* 3.8 31.4 - - + +
248B ASP 4.1 1.6 - - - +
250B ILE* 3.8 16.8 - - + +
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Residues in contact with CYS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.4 21.3 - - + -
77B ARG* 5.8 1.3 - - - -
91B ILE* 4.4 1.6 - - + -
139B CYS* 3.5 22.2 - - - -
140B HIS 3.7 3.8 - - - -
141B TYR* 3.6 31.4 - - - -
160B SER 3.1 20.0 + - - -
161B ALA* 3.3 9.2 - - - +
162B VAL 3.1 0.2 - - - -
163B PRO* 1.3 77.1 - - - +
165B ALA* 1.3 63.2 + - - +
167B MET* 3.3 3.8 + - - +
168B LEU* 3.1 27.6 + - - +
197B PHE* 3.9 12.9 - - + -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B MET* 3.5 19.6 - - + +
69B ASP* 4.0 10.3 - - - +
70B LEU* 3.8 37.2 - - + +
161B ALA 3.0 13.0 + - - +
162B VAL 3.5 6.7 - - - +
164B CYS* 1.3 74.9 - - - +
166B MET* 1.3 60.8 + - - +
168B LEU* 3.3 4.6 + - - +
169B GLU* 2.8 31.0 + - - +
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Residues in contact with MET 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B MET* 4.2 4.5 - - - -
162B VAL* 2.8 37.7 + - + +
163B PRO* 3.4 13.7 - - - +
165B ALA* 1.3 73.6 - - - +
167B MET* 1.3 60.1 + - - +
169B GLU* 3.3 1.8 + - - +
170B LEU* 2.9 30.1 + - - +
247B LEU* 4.1 20.0 - - + -
250B ILE* 3.7 21.1 - - + -
344B ILE* 4.1 11.7 - - + +
347B LEU* 3.7 33.9 - - + +
348B ASN* 3.2 29.2 - - - +
351B LEU* 4.6 11.1 - - + +
352B GLN* 5.4 0.2 + - - -
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Residues in contact with MET 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.5 38.6 - - + +
138B ALA* 3.7 14.6 - - - +
139B CYS* 3.5 29.4 - - - -
163B PRO 3.0 8.4 + - - +
164B CYS 3.3 5.8 + - - +
166B MET* 1.3 76.4 - - - +
168B LEU* 1.3 57.0 + - - +
170B LEU* 3.3 8.4 + - - +
171B ALA* 3.0 28.2 + - - +
195B LEU* 3.8 29.9 - - + +
196B ILE 3.6 16.2 - - - +
197B PHE* 3.8 17.9 - - + -
247B LEU* 4.3 13.2 - - + -
351B LEU* 5.5 1.1 - - + -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP* 3.6 35.7 - - + +
73B LEU* 4.7 1.6 - - + -
90B HIS* 4.0 22.0 - - + +
91B ILE* 4.0 24.0 - - + +
94B ARG* 4.1 11.7 - - + -
95B ILE* 3.8 33.9 - - + -
98B LEU* 4.9 1.4 - - - +
164B CYS 3.1 19.3 + - - +
165B ALA* 3.6 5.4 - - - +
166B MET 3.3 0.2 - - - -
167B MET* 1.3 77.6 - - - +
169B GLU* 1.3 57.5 + - - +
171B ALA* 3.4 6.6 + - + +
172B ARG* 3.0 26.7 + - - +
195B LEU* 5.7 0.4 - - + -
197B PHE* 4.1 12.1 - - + -
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Residues in contact with GLU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 2.6 30.1 + - - +
61B SER 3.1 17.8 + - - +
64B GLU* 5.1 0.5 - - - +
65B MET* 3.7 24.5 + - + +
69B ASP* 3.8 6.6 + - - +
165B ALA 2.8 17.6 + - - +
166B MET* 3.3 4.0 + - - +
168B LEU* 1.3 72.8 - - - +
170B LEU* 1.3 60.8 + - - +
172B ARG* 2.8 44.5 + - - -
173B ALA* 2.7 29.5 + - - +
348B ASN* 4.1 12.6 - - - +
352B GLN* 4.0 5.8 - - - +
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 4.0 13.5 - - + -
166B MET 2.9 18.1 + - - +
167B MET* 3.6 8.1 - - - +
169B GLU* 1.3 78.0 - - - +
171B ALA* 1.3 67.6 + - + +
174B LEU* 2.9 48.5 + - + +
178B LEU* 4.8 1.1 - - + -
193B LEU* 4.2 23.6 - - + -
195B LEU* 5.2 3.4 - - + -
351B LEU* 3.8 23.3 - - + -
352B GLN* 3.8 28.9 - - + +
355B VAL* 3.8 27.1 - - + -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 5.2 4.7 - - + -
98B LEU* 3.5 23.3 - - + +
102B TRP* 4.0 20.5 + - + +
167B MET 3.0 14.3 + - - +
168B LEU* 3.6 9.4 - - - +
169B GLU 3.3 0.2 - - - -
170B LEU* 1.3 81.9 - - - +
172B ARG* 1.3 61.9 + - - +
174B LEU 3.9 0.7 - - - -
175B ASP* 3.2 24.1 + - - +
178B LEU* 4.3 9.4 - - - +
195B LEU* 4.4 9.2 - - + -
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Residues in contact with ARG 172 (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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59B GLY 3.3 22.6 + - - -
61B SER* 3.8 13.8 - - - +
64B GLU* 5.1 10.4 - - - +
69B ASP* 5.2 1.8 - - - +
94B ARG* 4.3 18.8 - - - +
97B ARG* 4.4 10.8 - - - +
98B LEU* 3.8 25.1 - - + +
168B LEU 3.0 17.3 + - - +
169B GLU* 2.8 43.3 + - - +
171B ALA* 1.3 77.3 - - - +
173B ALA* 1.3 68.5 + - - +
175B ASP* 3.2 17.8 - - - +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLY* 3.7 19.8 - - - +
60B THR* 4.2 0.4 - - - -
169B GLU* 2.7 36.1 + - - +
170B LEU 4.1 0.2 - - - +
172B ARG* 1.3 84.7 - - - +
174B LEU* 1.3 63.2 + - - +
175B ASP 3.3 0.9 + - - -
176B LYS* 5.1 1.0 + - - +
177B LYS* 6.0 0.3 - - - +
352B GLN* 3.5 26.7 - - - +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 4.7 7.9 - - + -
170B LEU* 2.9 46.2 + - + +
171B ALA 3.9 1.3 - - - -
173B ALA* 1.3 81.3 - - - +
175B ASP* 1.3 59.0 + - - +
176B LYS 3.4 2.7 - - - -
177B LYS* 3.1 12.6 + - + +
178B LEU* 2.8 41.0 + - + +
352B GLN* 3.9 37.0 - - + +
355B VAL* 4.3 9.4 - - + -
356B LEU* 3.9 38.4 - - + -
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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
------------------------------------------------------------
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