Contacts of the strand formed by residues 111 - 117 (chain A) 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 VAL 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A VAL* 3.9 21.8 - - + -
103A PHE 3.2 8.7 - - - +
104A GLU* 4.0 20.0 - - + -
105A ALA 5.1 0.2 - - - +
109A GLU* 5.1 2.9 - - - -
110A LYS* 1.3 82.7 - - - +
112A SER* 1.3 63.0 + - - +
113A ASP* 5.3 2.8 - - + +
179C ASN 3.8 1.4 - - - +
180C ILE* 3.7 0.8 - - - -
181C LYS* 2.9 43.0 + - + +
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Residues in contact with SER 112 (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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81A CYS 5.1 2.9 + - - -
86A ASP* 5.5 0.5 + - - -
102A VAL* 3.4 7.4 - - - +
103A PHE* 2.8 45.3 + - - +
110A LYS* 4.0 11.1 - - - +
111A VAL* 1.3 73.4 - - - +
113A ASP* 1.3 62.7 + - - +
114A TYR* 3.4 29.1 + - - -
179C ASN 3.2 7.2 - - - -
180C ILE* 3.6 21.3 - - - +
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Residues in contact with ASP 113 (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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91A ARG* 4.2 7.6 + - - -
100A ALA* 5.1 2.8 - - - +
101A LEU 3.6 3.2 - - - +
102A VAL* 3.2 27.2 - - + +
111A VAL* 5.3 2.9 - - + +
112A SER* 1.3 76.9 - - - +
114A TYR* 1.3 71.6 + - - +
115A GLU* 5.3 3.1 - - - +
177C ASN* 4.1 4.3 - - - +
178C GLY* 3.7 1.2 - - - -
179C ASN* 2.7 45.7 + - + +
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Residues in contact with TYR 114 (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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78A ILE* 3.9 27.1 - - + -
81A CYS* 3.5 23.3 + - + +
100A ALA* 3.5 6.6 - - - +
101A LEU* 2.9 34.3 + - + +
103A PHE* 3.3 43.1 - + - -
112A SER* 3.4 14.5 + - - -
113A ASP* 1.3 82.0 - - - +
115A GLU* 1.3 62.6 + - - +
116A MET 4.0 0.9 - - - -
150C ASP* 4.7 1.2 - - - +
151C LEU* 4.5 3.1 - - + +
154C ILE* 3.9 29.4 - - + -
177C ASN* 3.4 4.9 - - - +
178C GLY* 3.4 27.6 - - - -
179C ASN 4.3 1.1 - - - -
180C ILE* 3.8 26.7 - - + +
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Residues in contact with GLU 115 (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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78A ILE* 4.8 1.1 - - - -
98A THR* 3.8 35.2 + - + +
99A LEU 3.4 6.3 - - - +
100A ALA* 5.2 6.7 - - + +
113A ASP* 5.3 3.4 - - - +
114A TYR* 1.3 75.3 - - - +
116A MET* 1.3 59.2 + - - +
117A LYS* 3.7 1.0 + - - +
176C GLY* 3.2 24.8 - - - -
177C ASN* 3.1 36.6 + - - +
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Residues in contact with MET 116 (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 VAL* 3.8 23.8 - - + -
71A ASN 4.7 0.9 - - - +
74A SER* 4.3 9.4 - - - -
75A MET* 3.5 48.5 - - + -
78A ILE* 3.5 20.6 - - + +
98A THR* 3.3 3.3 - - - -
99A LEU* 2.7 74.2 + - + +
101A LEU* 4.1 4.9 - - + +
114A TYR 4.0 1.0 - - - -
115A GLU* 1.3 73.9 - - - +
117A LYS* 1.3 74.0 + - - +
118A LEU* 3.5 3.3 + - + +
175C LEU 3.4 9.6 - - - +
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Residues in contact with LYS 117 (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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71A ASN* 5.5 4.7 + - - +
74A SER* 5.7 1.7 - - - -
97A ASP* 4.0 10.5 - - - +
98A THR* 4.3 10.5 - - + -
115A GLU 3.7 0.6 + - - +
116A MET* 1.3 84.1 - - - +
118A LEU* 1.3 67.6 + - - +
119A MET* 5.5 3.6 - - - +
173C GLY 4.2 9.4 + - - -
174C GLU* 3.1 34.0 + - - +
175C LEU* 2.8 19.9 + - - +
176C GLY* 4.0 8.7 - - - +
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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