Contacts of the strand formed by residues 176 - 183 (chain C) in PDB entry 1AXC
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 GLY 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLU 3.2 12.8 - - - -
117A LYS* 4.0 14.5 - - - +
154C ILE* 3.9 6.2 - - - +
172C SER* 3.6 0.7 - - - -
173C GLY* 2.8 33.6 + - - +
174C GLU 3.3 1.2 + - - -
175C LEU* 1.3 82.1 - - - +
177C ASN* 1.3 64.6 + - - +
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Residues in contact with ASN 177 (chain C).
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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78A ILE* 5.5 1.2 - - - +
113A ASP* 5.1 4.3 - - - +
114A TYR* 3.4 5.9 - - - +
115A GLU* 3.1 59.7 + - - +
154C ILE* 3.8 7.0 - - - -
171C ALA 3.2 14.6 - - - +
172C SER* 3.5 14.1 - - - +
175C LEU* 4.9 0.4 - - - +
176C GLY* 1.3 77.0 - - - +
178C GLY* 1.3 61.6 + - - +
179C ASN* 5.5 2.8 - - - +
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Residues in contact with GLY 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASP 3.7 0.9 - - - -
114A TYR* 3.4 24.9 - - - -
151C LEU* 4.4 5.6 - - - -
154C ILE* 3.5 8.7 - - - +
170C SER* 3.3 4.4 - - - -
171C ALA 2.8 34.9 + - - +
177C ASN* 1.3 77.3 - - - +
179C ASN* 1.3 62.2 + - - +
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Residues in contact with ASN 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL 3.8 1.2 - - - +
112A SER* 3.2 1.6 - - - -
113A ASP* 2.7 52.8 + - + +
114A TYR* 4.3 3.4 - - - -
151C LEU* 4.7 0.6 - - - +
168C LYS* 2.8 50.9 - - - +
169C PHE 3.2 6.6 - - - +
170C SER* 3.4 8.5 + - - +
177C ASN* 5.5 3.4 - - - +
178C GLY* 1.3 74.8 - - - +
180C ILE* 1.3 64.2 + - - +
181C LYS* 3.9 13.5 - - - +
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Residues in contact with ILE 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LYS* 3.5 39.0 - - + +
111A VAL 3.7 1.8 - - - +
112A SER* 3.6 15.5 - - - +
114A TYR* 3.8 16.4 - - - +
147C ILE* 3.9 39.9 - - + +
150C ASP* 5.1 6.1 - - + +
151C LEU* 3.6 26.5 - - + -
168C LYS* 3.4 4.0 - - - +
169C PHE* 2.7 41.4 + - + +
179C ASN* 1.3 80.6 + - - +
181C LYS* 1.3 62.3 + - - +
182C LEU* 5.0 0.9 - - + -
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Residues in contact with LYS 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU 3.2 2.4 - - - +
110A LYS* 3.1 6.3 - - - -
111A VAL* 2.9 45.9 + - + +
167C VAL 3.9 3.6 - - - +
168C LYS* 3.3 39.5 - - + +
179C ASN* 3.9 13.2 - - - +
180C ILE* 1.3 72.9 - - - +
182C LEU* 1.3 63.0 + - - +
183C SER* 5.0 3.0 + - - +
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Residues in contact with LEU 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU 3.3 2.7 - - - +
110A LYS* 3.6 33.2 - - + -
139C MET* 3.6 24.7 - - + -
143C GLU* 4.2 18.4 - - + +
147C ILE* 3.8 15.5 - - + -
166C GLY* 3.1 3.8 - - - -
167C VAL* 2.9 44.5 + - + +
169C PHE* 3.6 26.7 - - + -
180C ILE* 5.0 0.7 - - + -
181C LYS* 1.3 73.6 - - - +
183C SER* 1.3 63.5 + - - +
195C VAL* 4.8 19.1 - - + +
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A GLU* 2.9 36.6 + - - +
165C ASP 3.8 13.1 + - - -
166C GLY* 4.1 0.4 - - - -
181C LYS* 5.0 3.5 + - - +
182C LEU* 1.3 75.3 - - - +
184C GLN* 1.3 67.4 + - - +
185C THR* 3.1 5.9 + - - +
195C VAL* 3.8 13.1 - - - +
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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