Contacts of the helix formed by residues 142 - 150 (chain Y) in PDB entry 2CKV
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 GLU 142 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128Y VAL* 5.1 6.3 - - + +
137Y ASN* 3.6 8.4 + - - +
138Y TYR 3.3 9.8 + - - +
139Y SER* 3.1 10.2 + - - +
141Y ALA* 1.3 78.4 - - - +
143Y VAL* 1.3 56.6 + - + +
144Y VAL* 3.1 5.6 - - - -
145Y ASN* 3.1 30.5 + - + +
146Y HIS* 3.1 20.7 + - + -
172Y LEU* 4.7 4.8 - - + +
175Y VAL* 3.4 22.0 - - - +
181Y ASN* 2.9 43.3 + - - +
190Y SER* 3.4 15.5 + - - +
194Y ILE* 3.6 12.2 - - - +
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Residues in contact with VAL 143 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Y ILE* 5.0 3.4 - - + -
139Y SER 3.6 12.8 - - - +
140Y THR* 3.2 28.3 - - + +
142Y GLU* 1.3 73.8 - - + +
144Y VAL* 1.3 54.6 - - - +
145Y ASN 3.2 0.4 - - - -
146Y HIS* 3.5 20.0 - - + +
147Y PHE* 2.7 38.1 + - + +
190Y SER* 5.6 4.9 - - - +
193Y ASN* 5.8 5.4 - - + +
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Residues in contact with VAL 144 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Y PHE* 5.4 6.5 - - + +
106Y GLU* 4.3 5.6 - - + +
107Y ILE* 4.0 28.2 - - + +
110Y MET* 3.7 38.7 - - + +
121Y TYR* 5.4 2.7 - - + -
124Y LEU* 5.0 16.8 - - + -
140Y THR 4.2 1.4 + - - -
141Y ALA 3.2 25.4 - - - +
142Y GLU 4.2 0.2 - - - +
143Y VAL* 1.3 82.0 - - - +
145Y ASN* 1.3 68.3 + - - +
147Y PHE* 3.6 0.7 + - - -
148Y THR* 2.6 37.7 + - - +
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Residues in contact with ASN 145 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Y PHE* 5.6 0.4 - - - -
124Y LEU* 3.3 19.7 + - - +
125Y SER* 3.1 24.7 + - - -
128Y VAL* 3.5 40.3 - - - +
142Y GLU* 3.1 16.5 + - + +
144Y VAL* 1.3 86.4 - - - +
146Y HIS* 1.3 65.7 + - + +
148Y THR* 3.9 6.5 + - - -
149Y PRO* 3.4 9.4 - - - +
168Y ALA* 5.4 5.5 - - + +
171Y ALA* 5.9 1.1 - - - -
172Y LEU* 5.8 4.0 - - + -
197Y TYR* 3.3 26.5 + - + +
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Residues in contact with HIS 146 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142Y GLU* 3.1 31.4 + - + -
143Y VAL* 3.2 22.7 + - + +
145Y ASN* 1.3 80.4 - - + +
147Y PHE* 1.3 60.6 + - - +
149Y PRO* 3.4 7.5 - - - +
150Y GLU* 3.3 25.9 - - - +
172Y LEU* 3.6 13.9 - - + +
190Y SER* 4.4 7.0 - - - -
193Y ASN* 3.5 36.6 + - + +
194Y ILE* 3.6 28.9 - - + +
197Y TYR* 4.1 26.5 - + + -
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Residues in contact with PHE 147 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Y MET* 3.9 19.5 - - + -
111Y GLU 5.7 0.2 - - - -
112Y ALA* 3.2 39.0 - - + -
113Y HIS* 4.4 2.2 - - + -
143Y VAL* 2.7 21.1 + - + +
146Y HIS* 1.3 72.9 - - - +
148Y THR* 1.3 66.8 + - - +
149Y PRO 3.5 0.6 - - - -
150Y GLU* 3.2 39.8 + - - +
151Y ASN* 3.2 31.1 - - - +
155Y TYR* 4.7 2.6 - + - -
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Residues in contact with THR 148 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Y MET* 4.9 3.6 - - - +
121Y TYR* 3.4 46.4 - - + +
124Y LEU* 5.3 0.7 - - - +
144Y VAL* 2.6 23.4 + - - +
145Y ASN* 3.9 8.6 + - - -
147Y PHE* 1.3 76.0 - - - +
149Y PRO* 1.4 64.2 - - - +
155Y TYR* 3.2 32.8 - - + +
156Y PHE* 3.5 31.4 - - + -
164Y THR* 5.7 0.2 - - + -
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Residues in contact with PRO 149 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145Y ASN 3.4 10.8 - - - +
146Y HIS 3.4 5.8 - - - +
148Y THR* 1.4 94.9 - - - +
150Y GLU* 1.3 64.5 + - - +
151Y ASN 3.3 12.1 + - - +
154Y TYR* 4.7 13.5 - - + +
155Y TYR* 5.2 2.5 - - + +
156Y PHE* 3.6 31.2 - - + -
197Y TYR* 3.1 31.0 - - + +
201Y LEU* 6.4 1.8 - - + -
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Residues in contact with GLU 150 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146Y HIS* 3.3 23.9 - - - +
147Y PHE* 3.2 48.4 - - + +
148Y THR 3.6 1.0 - - - -
149Y PRO* 1.3 81.1 - - - +
151Y ASN* 1.3 72.8 + - - +
152Y LYS* 3.8 0.9 + - - -
197Y TYR* 6.1 1.8 - - + -
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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