Contacts of the helix formed by residues 153 - 166 (chain A) in PDB entry 1C1Y
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 ASN 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.8 28.1 - - + +
145A GLU 2.9 26.4 + - - +
146A SER* 4.0 1.8 - - - -
151A LYS 4.1 1.4 + - - -
152A ILE* 1.3 82.6 - - - +
154A VAL* 1.3 61.9 + - - +
156A GLU* 3.2 29.0 + - - +
157A ILE* 3.3 24.9 + - - +
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Residues in contact with VAL 154 (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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19A LEU* 3.8 30.5 - - + +
22A GLN* 4.0 15.9 - - + -
23A PHE* 3.8 22.9 - - + +
147A SER 3.6 24.2 - - - +
148A ALA* 4.3 5.8 - - - -
151A LYS* 3.9 17.9 - - + -
152A ILE 3.2 2.7 - - - +
153A ASN* 1.3 75.6 - - - +
155A ASN* 1.3 72.7 + - - +
156A GLU* 3.3 1.5 + - - -
157A ILE* 3.3 17.6 + - - +
158A PHE* 3.6 14.9 - - + -
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Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.3 28.1 - - - +
42A LYS* 5.0 3.8 + - - +
154A VAL* 1.3 83.9 - - - +
156A GLU* 1.3 72.2 + - - +
158A PHE* 3.1 6.4 + - - +
159A TYR* 2.9 61.1 + - + -
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Residues in contact with GLU 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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112A ILE* 4.6 0.3 - - - +
144A LEU* 3.8 19.9 - - + +
153A ASN* 3.2 35.4 + - - +
154A VAL 3.2 0.7 + - - -
155A ASN* 1.3 83.5 + - - +
157A ILE* 1.3 62.7 + - - +
159A TYR* 4.1 11.1 - - + +
160A ASP* 3.0 28.2 + - - +
163A ARG* 5.0 1.7 + - - +
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Residues in contact with ILE 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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19A LEU* 4.0 28.5 - - + -
79A ALA* 4.0 17.3 - - + -
81A VAL* 5.8 0.2 - - + -
112A ILE* 4.0 28.7 - - + +
114A VAL* 3.7 26.0 - - + -
144A LEU* 4.0 16.1 - - + +
146A SER* 4.1 1.3 - - - +
153A ASN 3.3 19.3 - - - +
154A VAL 3.6 9.0 - - - +
155A ASN 3.2 0.4 + - - -
156A GLU* 1.3 79.0 - - - +
158A PHE* 1.3 78.4 + - + +
160A ASP* 4.0 2.1 - - - +
161A LEU* 3.4 22.3 + - + +
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Residues in contact with PHE 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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6A LEU* 3.7 23.2 - - + +
8A VAL* 4.1 19.7 - - + -
19A LEU* 4.4 9.2 - - + -
20A THR* 4.3 15.0 - - - -
23A PHE* 3.5 52.0 - + + -
53A LEU* 4.2 7.0 - - + -
55A ILE* 3.8 31.4 - - + -
79A ALA* 5.5 0.4 - - + -
154A VAL* 3.6 16.2 - - + -
155A ASN 3.1 4.7 + - - +
157A ILE* 1.3 94.0 - - + +
159A TYR* 1.3 67.0 + - - +
160A ASP 3.2 0.2 - - - -
161A LEU* 3.2 9.0 + - + +
162A VAL* 3.2 26.4 + - - +
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Residues in contact with TYR 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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23A PHE* 3.9 16.3 - + - -
42A LYS* 5.4 1.9 + - - -
44A VAL* 3.3 34.0 - - + +
45A GLU 4.6 9.0 + - - -
46A VAL* 3.9 22.0 - - + +
53A LEU* 5.7 0.4 - - + -
155A ASN* 2.9 50.5 + - + +
156A GLU* 4.1 9.6 - - + +
158A PHE* 1.3 76.1 - - - +
160A ASP* 1.3 63.3 + - - +
162A VAL* 3.3 7.2 + - - +
163A ARG* 3.2 51.5 + - - +
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Residues in contact with ASP 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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112A ILE* 4.1 13.8 - - + +
142A ALA* 3.7 12.9 - - - +
144A LEU* 6.1 0.2 - - + -
156A GLU 3.0 19.3 + - - +
157A ILE 4.0 3.4 - - - +
159A TYR* 1.3 76.2 - - - +
161A LEU* 1.3 64.5 + - - +
163A ARG* 3.2 22.4 + - - +
164A GLN* 2.7 54.2 + - - +
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Residues in contact with LEU 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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6A LEU* 3.9 32.3 - - + -
7A VAL 5.4 0.7 - - - +
77A GLY* 4.2 2.5 - - - +
78A PHE 3.6 44.0 - - - +
79A ALA* 4.2 8.7 - - + +
110A PRO 4.1 4.5 - - - +
111A MET* 3.7 20.6 - - - +
112A ILE* 3.8 13.7 - - + -
157A ILE* 3.4 16.3 + - + +
158A PHE* 3.2 12.4 + - + +
160A ASP* 1.3 78.4 - - - +
162A VAL* 1.3 57.7 + - - +
164A GLN* 3.3 9.6 + - - +
165A ILE* 3.0 35.5 + - + +
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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
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4A TYR* 3.7 27.9 - - + +
6A LEU* 4.8 4.9 - - + -
46A VAL* 4.0 25.6 - - + -
51A CYS* 4.2 7.6 - - - -
53A LEU* 3.9 32.1 - - + -
158A PHE 3.2 14.5 + - - +
159A TYR 3.4 7.4 - - - +
160A ASP 3.2 0.2 - - - -
161A LEU* 1.3 76.7 - - - +
163A ARG* 1.3 61.9 + - - +
165A ILE* 3.1 10.5 + - - +
166A ASN* 2.9 38.1 + - - +
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Residues in contact with ARG 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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46A VAL* 4.6 6.9 - - + +
47A ASP* 3.2 38.9 + - - +
156A GLU* 5.0 2.4 + - - +
159A TYR* 3.2 50.8 + - - +
160A ASP* 3.2 23.8 + - - +
162A VAL* 1.3 77.1 - - - +
164A GLN* 1.3 61.7 + - + +
166A ASN* 2.7 28.2 + - - +
167A ARG* 3.7 8.3 + - - +
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Residues in contact with GLN 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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110A PRO* 3.3 19.9 - - + +
111A MET 3.1 45.3 + - - +
112A ILE* 4.5 0.4 - - - +
142A ALA* 3.8 9.1 - - - +
160A ASP* 2.7 35.7 + - - +
161A LEU* 3.6 14.2 - - - +
163A ARG* 1.3 76.5 - - + +
165A ILE* 1.3 63.6 + - - +
167A ARG* 3.1 19.4 + - - +
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Residues in contact with ILE 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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2A ARG* 5.5 3.8 - - - +
4A TYR* 3.6 35.0 - - + -
6A LEU* 3.7 25.1 - - + -
76A GLN* 3.8 34.8 - - + +
77A GLY* 4.0 6.1 - - - +
110A PRO* 4.2 20.9 - - + -
161A LEU 3.0 21.9 + - - +
162A VAL* 3.1 6.5 + - - +
164A GLN* 1.3 71.4 - - - +
166A ASN* 1.3 58.4 + - - +
167A ARG* 2.7 24.5 + - - +
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Residues in contact with ASN 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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2A ARG* 6.6 0.4 - - - -
4A TYR* 3.7 21.2 + - + +
46A VAL* 5.9 0.3 - - - +
47A ASP* 5.8 2.0 + - - -
162A VAL* 2.9 22.3 + - - +
163A ARG* 2.7 33.7 + - - +
165A ILE* 1.3 72.6 - - - +
167A ARG* 1.3 71.7 + - - +
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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