Contacts of the helix formed by residues 160 - 174 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ARG* 3.7 7.3 - - - +
139A CYS* 4.7 0.7 - - - -
140A HIS* 3.3 37.5 + - - -
156A GLY 3.4 0.4 + - - -
158A THR 3.4 6.6 + - - -
159A ASP* 1.4 71.2 + - - +
161A ALA* 1.3 66.3 + - - +
162A VAL 3.2 2.5 - - - -
163A PRO* 3.2 15.1 - - - +
164A CYS* 3.0 23.7 + - - -
248A ASP* 2.7 30.3 + - - -
249A LEU 3.6 2.6 + - - -
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Residues in contact with ALA 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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70A LEU* 3.7 8.9 - - + +
73A LEU* 4.1 13.8 - - + +
74A LEU* 3.7 24.0 - - + -
77A ARG* 3.4 18.7 - - - +
156A GLY 3.1 12.7 + - - +
157A ALA 3.3 8.0 + - - +
160A SER* 1.3 76.0 - - - +
162A VAL* 1.3 64.0 + - - +
164A CYS* 3.2 10.0 + - - +
165A ALA* 2.9 23.7 + - - +
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MET* 5.4 2.0 - - + -
70A LEU* 3.9 14.8 - - + -
157A ALA 2.8 17.9 + - - +
161A ALA* 1.3 72.7 - - - +
163A PRO* 1.3 67.9 - - - +
165A ALA* 3.0 4.6 + - - +
166A MET* 2.8 45.3 + - - +
250A ILE 3.3 25.1 - - - +
339A LEU* 3.6 36.6 - - + -
344A ILE* 3.9 29.2 - - + -
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Residues in contact with PRO 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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139A CYS* 3.7 23.1 - - + -
158A THR 3.5 14.4 - - - +
160A SER* 3.2 26.9 - - - +
162A VAL* 1.3 95.2 - - + +
164A CYS* 1.3 63.7 + - - +
166A MET* 3.2 11.3 + - - +
167A MET* 3.0 27.4 + - - +
247A LEU* 3.8 20.1 - - + +
248A ASP* 4.2 2.2 - - - -
250A ILE* 3.9 20.0 - - + +
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Residues in contact with CYS 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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73A LEU* 3.5 21.8 - - + -
77A ARG* 5.7 0.9 - - - -
91A ILE* 4.4 1.6 - - + -
139A CYS* 3.5 24.9 - - - -
140A HIS 3.7 4.0 - - - -
141A TYR* 3.6 30.1 - - - -
160A SER 3.0 18.1 + - - -
161A ALA* 3.4 10.1 - - - +
162A VAL 3.1 0.2 - - - -
163A PRO* 1.3 75.6 - - - +
165A ALA* 1.3 62.9 + - - +
167A MET* 3.2 5.2 + - - +
168A LEU* 3.0 27.5 + - + +
197A PHE* 3.9 13.8 - - + -
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MET* 3.6 17.7 - - + +
69A ASP* 3.9 10.3 - - - +
70A LEU* 3.7 40.2 - - + +
73A LEU* 4.4 0.4 - - + +
161A ALA 2.9 15.2 + - - +
162A VAL 3.6 3.8 - - - +
164A CYS* 1.3 76.9 - - - +
166A MET* 1.3 57.6 + - - +
168A LEU* 3.3 4.8 + - - +
169A GLU* 2.8 30.8 + - - +
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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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65A MET* 4.1 4.5 - - - -
162A VAL* 2.8 28.8 + - - +
163A PRO* 3.2 13.9 + - - +
165A ALA* 1.3 72.8 - - - +
167A MET* 1.3 59.1 + - - +
169A GLU* 3.8 1.7 - - - +
170A LEU* 2.9 28.8 + - - +
247A LEU* 4.2 18.4 - - + -
250A ILE* 3.7 30.1 - - + -
344A ILE* 4.0 16.4 - - + +
347A LEU* 3.8 34.5 - - + +
348A ASN* 3.2 28.7 - - - +
351A LEU* 4.7 11.0 - - + +
352A GLN* 5.3 0.2 + - - -
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Residues in contact with MET 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.5 38.1 - - + +
138A ALA* 3.7 15.7 - - - +
139A CYS* 3.5 29.4 - - - -
163A PRO 3.0 8.5 + - - +
164A CYS 3.5 5.8 - - - +
166A MET* 1.3 76.4 - - - +
168A LEU* 1.3 63.1 + - - +
170A LEU* 3.3 8.8 + - - +
171A ALA* 3.0 22.9 + - - +
195A LEU* 3.8 23.6 - - + +
196A ILE 3.5 15.9 - - - +
197A PHE* 3.7 25.8 - - + -
247A LEU* 4.3 13.5 - - + -
351A LEU* 5.6 0.7 - - + -
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Residues in contact with LEU 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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69A ASP* 3.5 37.1 - - + +
73A LEU* 4.6 1.6 - - + -
90A HIS* 4.1 17.9 - - + +
91A ILE* 4.0 28.0 - - + +
94A ARG* 4.1 12.1 - - + -
95A ILE* 3.8 32.5 - - + -
98A LEU* 5.0 1.4 - - - +
164A CYS 3.0 20.4 + - - +
165A ALA 3.7 3.1 - - - +
167A MET* 1.3 78.3 - - - +
169A GLU* 1.3 57.1 + - - +
171A ALA* 3.3 6.7 + - + +
172A ARG* 3.0 27.0 + - - +
195A LEU* 5.7 0.9 - - + -
197A PHE* 4.2 12.3 - - + -
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Residues in contact with GLU 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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60A THR* 2.6 31.7 + - - +
61A SER 3.0 15.5 + - - +
64A GLU 5.2 0.7 - - - -
65A MET* 3.7 25.7 + - + +
69A ASP* 3.9 6.4 + - - +
165A ALA 2.8 18.5 + - - +
166A MET* 4.0 3.6 - - - +
168A LEU* 1.3 72.9 - - - +
170A LEU* 1.3 60.2 + - - +
172A ARG* 2.9 43.8 + - - -
173A ALA* 2.8 29.1 + - - +
348A ASN* 4.0 12.6 - - - +
352A GLN* 3.9 5.4 - - - +
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.9 18.4 - - + -
166A MET 2.9 18.3 + - - +
167A MET* 3.6 7.9 - - - +
168A LEU 3.2 0.2 - - - -
169A GLU* 1.3 73.3 - - - +
171A ALA* 1.3 73.1 + - - +
174A LEU* 2.9 48.1 + - + +
178A LEU* 4.9 1.1 - - + -
193A LEU* 4.3 20.0 - - + -
195A LEU* 5.1 3.4 - - + -
351A LEU* 3.8 20.4 - - + -
352A GLN* 3.8 33.4 - - + +
355A VAL* 3.7 27.6 - - + -
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Residues in contact with ALA 171 (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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95A ILE* 5.3 4.7 - - + -
98A LEU* 3.6 22.2 - - + +
102A TRP* 4.1 20.3 + - + +
167A MET 3.0 14.0 + - - +
168A LEU* 3.3 9.2 + - - +
170A LEU* 1.3 82.4 - - + +
172A ARG* 1.3 62.3 + - - +
174A LEU 3.8 0.7 - - - -
175A ASP* 3.1 25.5 + - - +
178A LEU* 4.3 9.8 - - - +
195A LEU* 4.5 9.0 - - + -
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Residues in contact with ARG 172 (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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59A GLY 3.3 22.6 + - - -
61A SER* 3.9 13.6 - - - +
64A GLU* 5.2 11.1 - - - +
69A ASP* 5.2 2.0 - - - +
94A ARG* 4.3 18.6 - - - +
97A ARG* 4.5 9.2 - - - +
98A LEU* 3.8 25.0 - - + +
168A LEU 3.0 16.1 + - - +
169A GLU* 2.9 42.6 + - - +
171A ALA* 1.3 75.2 - - - +
173A ALA* 1.3 71.2 + - - +
175A ASP* 3.1 17.5 + - - +
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Residues in contact with ALA 173 (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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59A GLY* 3.6 24.1 - - - +
60A THR* 4.2 0.2 - - - -
169A GLU* 2.8 31.8 + - - +
170A LEU 4.2 0.2 - - - +
172A ARG* 1.3 84.4 - - - +
174A LEU* 1.3 62.8 + - + +
175A ASP 3.3 0.7 + - - -
176A LYS 5.1 1.4 + - - -
177A LYS* 5.9 0.5 - - - +
352A GLN* 3.5 26.5 - - - +
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Residues in contact with LEU 174 (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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56A ILE* 4.6 9.2 - - + -
170A LEU* 2.9 44.1 + - + +
171A ALA 3.8 1.6 - - - -
173A ALA* 1.3 81.5 - - + +
175A ASP* 1.3 59.8 + - - +
176A LYS 3.3 2.7 - - - -
177A LYS* 3.1 12.4 + - + +
178A LEU* 2.8 40.2 + - + +
352A GLN* 4.1 28.3 - - + +
355A VAL* 4.3 8.7 - - + -
356A LEU* 3.8 45.8 - - + -
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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