Contacts of the helix formed by residues 173 - 181 (chain A) in PDB entry 4KYI
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 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A MET* 5.1 5.2 - - + -
90A ASP* 3.5 51.6 - - + +
93A LYS* 5.0 6.5 - - + +
94A LEU* 4.1 27.8 - - + +
128A MET* 3.9 23.3 - - + -
129A GLN* 5.2 0.2 - - - +
132A LYS* 5.3 3.6 - - - +
172A ASN* 1.3 78.5 + - - +
174A ASP* 1.3 62.7 + - - +
175A ASP 3.1 4.7 - - - -
176A ILE* 3.0 26.1 + - + +
177A ILE* 3.4 13.5 + - + +
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Residues in contact with ASP 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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93A LYS* 3.1 41.3 + - - +
172A ASN* 3.5 20.1 + - - +
173A VAL* 1.3 76.2 - - - +
175A ASP* 1.3 61.1 + - - +
176A ILE 3.3 0.2 - - - -
177A ILE* 3.6 18.9 - - + +
178A ASN* 3.0 33.4 + - - +
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Residues in contact with ASP 175 (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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169A VAL* 3.7 9.7 - - - +
170A ILE* 3.7 22.2 - - + +
171A ASN* 3.6 11.4 - - - +
172A ASN* 3.4 41.5 + - - +
173A VAL 3.1 0.4 - - - -
174A ASP* 1.3 77.8 - - - +
176A ILE* 1.3 61.8 + - - +
178A ASN* 2.8 23.0 + - - +
179A LEU* 3.2 14.2 - - - +
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Residues in contact with ILE 176 (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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94A LEU* 5.0 8.3 - - + -
98A LEU* 6.0 1.6 - - + -
121A ILE* 4.0 28.7 - - + -
124A VAL* 3.8 17.7 - - + +
125A ILE* 3.7 39.9 - - + -
128A MET* 4.2 19.5 - - + -
170A ILE* 3.7 18.8 - - + -
172A ASN 3.8 2.5 - - - +
173A VAL* 3.0 17.0 + - + +
175A ASP* 1.3 75.6 - - - +
177A ILE* 1.3 65.1 + - - +
179A LEU* 3.2 20.6 - - + +
180A THR* 3.3 10.5 - - + +
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Residues in contact with ILE 177 (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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93A LYS* 3.3 35.0 - - + +
94A LEU* 4.5 13.5 - - + -
97A GLY* 3.5 24.7 - - - +
98A LEU* 5.6 3.4 - - + -
173A VAL* 3.4 11.6 + - + +
174A ASP* 3.6 28.7 - - - +
175A ASP 3.3 0.4 - - - -
176A ILE* 1.3 75.9 - - - +
178A ASN* 1.3 60.0 + - + +
180A THR* 2.4 36.5 + - - +
181A LYS* 3.6 24.0 + - - +
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Residues in contact with ASN 178 (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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174A ASP* 3.0 16.9 + - - +
175A ASP* 2.8 35.6 + - - +
177A ILE* 1.3 74.4 - - + +
179A LEU* 1.3 68.5 + - - +
180A THR 3.2 0.4 - - - -
181A LYS* 3.0 34.4 + - + +
182A SER* 3.5 9.5 + - - -
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Residues in contact with LEU 179 (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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121A ILE* 4.7 5.8 - - + -
124A VAL* 4.8 8.5 - - + -
163A LEU* 6.1 0.7 - - + -
168A ILE* 4.1 19.7 - - + -
170A ILE* 3.9 26.7 - - + -
175A ASP 3.2 13.4 + - - +
176A ILE* 3.2 13.0 - - - +
178A ASN* 1.3 83.1 + - - +
180A THR* 1.3 62.0 + - + +
182A SER* 3.1 22.7 + - - +
185A ASP* 3.6 35.3 - - + +
186A LEU* 3.3 19.4 - - + +
189A LEU* 4.3 20.4 - - + -
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Residues in contact with THR 180 (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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97A GLY 5.3 1.0 + - - -
98A LEU* 3.8 24.1 - - + +
102A LYS* 3.8 23.5 - - - +
103A LEU* 3.7 26.5 - - + -
121A ILE* 4.1 13.5 - - + -
176A ILE 3.3 16.4 - - - +
177A ILE* 2.4 24.8 + - - +
179A LEU* 1.3 76.1 - - - +
181A LYS* 1.3 62.1 + - - +
182A SER 3.1 5.1 + - - -
183A VAL* 5.8 1.0 - - - +
186A LEU* 3.7 23.0 - - - +
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Residues in contact with LYS 181 (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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97A GLY* 5.0 6.9 + - - -
99A ASP* 5.7 2.6 + - - -
102A LYS* 4.4 18.8 + - - +
177A ILE* 3.6 35.6 - - - +
178A ASN* 3.0 22.2 + - + +
180A THR* 1.3 80.2 + - - +
182A SER* 1.3 58.8 + - - +
183A VAL* 4.2 2.3 + - - +
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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