Contacts of the helix formed by residues 145 - 158 (chain F) in PDB entry 5ANC
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 LEU 145 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48F LEU* 3.8 17.0 - - + -
50F VAL* 5.8 2.9 - - + -
142F ASP* 3.4 35.9 - - - +
143F ASN 3.7 6.4 + - - +
144F MET* 1.3 72.3 - - - +
146F ALA* 1.3 78.5 + - + +
147F ASN* 3.1 4.3 + - - +
148F VAL* 3.3 10.0 - - + +
149F VAL* 3.0 38.1 + - + +
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Residues in contact with ALA 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F LEU* 1.3 88.5 - - + +
147F ASN* 1.3 65.8 + - - +
149F VAL* 3.5 11.7 - - - +
150F GLU* 3.1 27.9 - - - +
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Residues in contact with ASN 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F TYR* 3.6 17.8 - - + -
78F LYS 4.9 3.0 + - - -
79F THR* 3.2 48.5 + - + +
143F ASN 4.8 0.7 - - - +
144F MET* 3.3 29.4 - - + +
145F LEU 3.1 1.1 - - - -
146F ALA* 1.3 86.0 - - - +
148F VAL* 1.3 60.8 - - - +
150F GLU* 3.2 5.7 + - - +
151F ALA* 3.0 23.2 + - - +
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Residues in contact with VAL 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LEU* 5.6 0.2 - - + -
50F VAL* 3.7 29.4 - - + -
79F THR* 4.5 8.3 - - + -
85F PHE* 5.0 7.6 - - + -
138F ILE* 4.1 22.9 - - + +
140F THR* 4.3 15.0 - - + -
144F MET* 3.9 28.0 - - + +
145F LEU* 3.3 21.3 - - - +
147F ASN* 1.3 74.6 - - - +
149F VAL* 1.3 62.0 + - - +
151F ALA* 3.2 10.0 + - - +
152F LEU* 2.9 31.4 + - - +
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Residues in contact with VAL 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F VAL* 4.4 9.4 - - + -
145F LEU* 3.0 24.0 - - + +
146F ALA* 3.5 17.9 - - + +
148F VAL* 1.3 84.1 - - + +
150F GLU* 1.3 59.6 + - + +
152F LEU* 3.3 10.4 - - + +
153F ARG* 2.8 32.3 + - - +
165F ILE* 3.9 27.6 - - + +
167F VAL* 5.6 5.2 - - + -
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Residues in contact with GLU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F TYR* 4.0 23.2 + - + +
146F ALA 3.1 19.7 - - - +
147F ASN 3.2 9.7 + - - +
149F VAL* 1.3 79.8 - - + +
151F ALA* 1.3 63.6 + - - +
153F ARG* 2.6 50.3 + - - +
154F ARG* 3.0 23.4 + - - +
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Residues in contact with ALA 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F SER* 4.2 0.7 - - - -
72F CYS* 3.8 23.6 - - + +
75F TYR* 3.7 34.4 - - + +
85F PHE* 5.5 2.5 - - + -
138F ILE* 5.2 2.7 - - + -
147F ASN 3.0 10.8 + - - +
148F VAL* 3.2 12.3 + - - +
150F GLU* 1.3 75.8 - - - +
152F LEU* 1.3 53.0 + - - +
154F ARG* 3.2 9.9 + - - +
155F SER* 2.7 34.6 + - - -
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Residues in contact with LEU 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F VAL* 3.7 24.5 - - + -
51F HIS 3.9 8.1 - - - +
52F LEU* 3.9 32.2 - - + +
72F CYS* 4.9 2.0 - - - -
136F PHE* 4.3 11.7 - - + +
137F SER* 6.2 0.2 - - - -
138F ILE* 4.1 16.8 - - + -
148F VAL 2.9 15.6 + - - +
149F VAL* 3.3 11.2 - - - +
151F ALA* 1.3 73.1 - - - +
153F ARG* 1.3 54.0 + - - +
155F SER* 3.0 9.1 + - - +
156F SER* 2.6 39.9 + - - -
165F ILE* 3.5 39.5 - - + -
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Residues in contact with ARG 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F TYR* 4.5 11.1 + - - -
149F VAL 2.8 18.1 + - - +
150F GLU* 2.6 46.4 + - - +
152F LEU* 1.3 71.5 - - - +
154F ARG* 1.3 91.1 + - - +
156F SER* 3.1 20.4 - - - -
157F TYR* 3.0 48.7 + - + +
165F ILE* 4.4 3.5 - - + +
3169N C 3.9 1.0 + - - -
3170N A 2.9 32.3 + - - -
3171N A 5.8 0.2 + - - -
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Residues in contact with ARG 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE 4.5 1.4 + - - -
71F SER* 3.5 48.5 + - - +
74F LYS* 4.2 5.5 - - - +
75F TYR* 3.9 25.1 - - - +
150F GLU 3.0 11.7 + - - +
151F ALA* 3.3 8.5 - - - +
153F ARG* 1.3 101.2 - - - +
155F SER* 1.3 64.0 + - - +
157F TYR* 3.1 24.3 + - - +
158F LYS* 3.2 18.2 + - - +
3169N C 4.1 2.8 + - - +
3170N A 3.4 36.1 + - - -
3171N A 3.6 39.1 + - - -
3184N A 3.8 14.6 - - - +
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Residues in contact with SER 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F LEU* 4.0 16.2 - - - -
68F GLY* 3.7 11.6 + - - -
71F SER* 4.2 2.3 + - - -
72F CYS* 3.1 23.1 - - - -
136F PHE* 4.9 2.2 - - - -
151F ALA 2.7 20.3 + - - -
152F LEU* 3.1 14.9 - - - -
154F ARG* 1.3 78.2 - - - +
156F SER* 1.3 59.2 + - - +
158F LYS* 3.0 19.4 + - - +
159F PHE* 3.3 24.5 + - - -
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Residues in contact with SER 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F LEU* 4.3 10.2 - - - +
152F LEU 2.6 28.8 + - - -
153F ARG* 3.1 19.0 + - - -
155F SER* 1.3 71.0 - - - +
157F TYR* 1.3 62.6 + - - +
159F PHE* 3.2 21.5 + - - +
161F GLY 5.0 0.5 - - - +
163F GLN* 3.9 26.2 + - - +
165F ILE* 4.5 5.7 - - - +
1440N A 5.6 2.7 + - - -
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Residues in contact with TYR 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ARG* 3.0 64.1 + - + +
154F ARG* 3.1 9.4 + - - +
156F SER* 1.3 78.6 - - - +
158F LYS* 1.3 59.9 + - + +
159F PHE 3.1 7.3 + - - +
1439N A 5.7 2.6 + - - -
1440N A 3.5 39.0 - - - -
1441N G 3.1 16.1 + - - -
3168N C 4.5 2.5 - - - +
3169N C 2.9 61.0 - - + +
3170N A 5.0 0.3 + - - -
3186N G 3.8 16.7 + - - +
3187N C 4.2 6.4 + - - -
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Residues in contact with LYS 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F ALA* 4.1 4.3 - - - +
67F ALA* 3.6 22.9 - - + +
68F GLY* 4.3 13.9 - - - +
71F SER* 3.4 21.5 - - - +
154F ARG* 3.2 20.4 - - - +
155F SER* 3.0 8.4 + - - +
157F TYR* 1.3 78.1 - - + +
159F PHE* 1.3 68.3 + - - +
3169N C 4.2 25.2 + - - +
3170N A 5.7 1.6 + - - -
3184N A 4.5 8.9 - - - +
3185N C 3.2 41.7 + - - +
3186N G 2.7 38.2 + - - +
3187N C 4.2 3.2 - - - +
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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