Contacts of the helix formed by residues 122 - 128 (chain K) in PDB entry 2WQT
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 THR 122 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120K ASP 3.8 8.5 - - - +
121K ILE* 1.3 78.6 - - - +
123K PHE* 1.3 66.3 + - - +
124K ASP* 2.8 23.3 + - - +
125K GLU* 2.9 43.1 + - - +
126K LEU* 3.0 12.0 + - - +
209K VAL* 4.3 3.8 - - - -
213K ARG* 4.3 3.6 - - - +
57L VAL* 4.7 3.3 - - + +
84L ALA* 3.7 35.9 - - + +
87L CYS* 3.8 13.2 - - + -
164L TYR* 4.9 1.8 - - - +
1T MET* 4.7 1.1 - - + -
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Residues in contact with PHE 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122K THR* 1.3 72.4 - - - +
124K ASP* 1.3 61.2 + - - +
126K LEU* 3.4 4.5 + - - +
127K TYR* 3.3 31.4 + + - -
203K HIS* 3.8 28.7 - + - -
205K LEU* 3.5 30.9 - - + +
206K ASN* 3.4 26.9 - - - -
209K VAL* 3.8 15.6 - - + +
213K ARG* 5.2 0.6 - - - +
87L CYS* 4.2 12.5 + - - -
88L TYR 4.6 0.4 - - - +
89L GLY* 3.4 18.2 - - - +
90L ASP* 3.7 15.3 - - + -
166L ILE* 3.5 31.2 - - + -
167L GLY 3.5 16.2 - - - -
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Residues in contact with ASP 124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122K THR* 2.8 22.2 + - - -
123K PHE* 1.3 80.2 - - - +
125K GLU* 1.3 79.1 + - - +
127K TYR* 3.3 23.8 - - - +
128K ASN* 3.6 6.6 + - - +
57L VAL* 6.1 0.5 - - - +
87L CYS* 3.7 3.5 - - - -
111L VAL* 4.6 17.6 - - + +
132L TRP* 5.4 3.3 - - - -
134L LEU* 4.9 5.6 - - + +
164L TYR* 4.2 4.2 + - - -
166L ILE* 3.7 30.6 - - + +
225L GLY 5.1 4.9 - - - +
227L ILE* 3.8 28.3 - - + +
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Residues in contact with GLU 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K ARG* 5.8 0.5 + - - -
116K LEU* 5.5 0.2 - - - +
118K ALA* 5.5 1.2 - - - +
121K ILE* 3.4 17.5 - - + +
122K THR* 2.9 37.2 + - - +
124K ASP* 1.3 82.7 - - - +
126K LEU* 1.3 66.0 + - - +
128K ASN* 3.3 16.4 + - - +
129K ALA* 3.6 9.7 + - - +
55L ARG* 3.0 39.6 + - - -
57L VAL* 3.9 11.1 - - - +
225L GLY 5.7 4.7 - - - +
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Residues in contact with LEU 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K LEU* 4.7 1.6 - - + -
112K LEU* 5.2 6.5 - - + -
116K LEU* 4.2 23.3 - - + -
121K ILE* 4.1 12.4 - - + +
122K THR 3.0 11.2 + - - +
123K PHE 3.6 8.1 - - - +
125K GLU* 1.3 75.1 - - - +
127K TYR* 1.3 65.2 + - - +
129K ALA* 2.8 19.4 + - + +
130K ILE* 3.4 12.7 + - + +
205K LEU* 3.7 36.6 - - + +
208K ALA* 3.5 47.8 - - + +
209K VAL* 4.0 11.0 - - + +
212K ALA* 4.4 1.3 - - + -
228K ILE* 5.6 0.7 - - + -
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Residues in contact with TYR 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K PHE* 3.3 27.1 + + - -
124K ASP* 3.3 13.1 + - - +
125K GLU 3.3 0.2 - - - -
126K LEU* 1.3 79.9 - - - +
128K ASN* 1.3 61.9 + - - +
129K ALA 3.1 1.4 + - - -
130K ILE* 3.3 26.2 + - + +
173K PRO* 4.6 17.7 - - + +
176K LEU 4.7 1.3 + - - -
178K LEU* 4.3 18.7 + - + +
203K HIS* 4.5 6.4 + - - -
205K LEU* 3.6 24.8 - - + +
132L TRP* 4.5 15.4 - + + +
134L LEU* 3.7 21.1 - - + -
167L GLY 3.5 20.4 + - - -
168L GLY* 3.6 12.6 - - - -
169L PRO* 3.8 3.7 - - + +
170L ALA* 3.6 38.2 + - + -
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Residues in contact with ASN 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K ASN* 2.6 24.8 + - - -
114K ARG* 3.1 32.5 + - - +
124K ASP 3.6 5.9 + - - +
125K GLU* 3.3 11.6 + - - +
126K LEU 3.1 0.8 - - - -
127K TYR* 1.3 79.2 - - - +
129K ALA* 1.3 50.3 + - - +
130K ILE 3.5 1.6 - - - +
111L VAL* 6.1 2.0 - - + -
131L GLU* 2.9 32.8 + - - +
132L TRP* 2.8 36.7 - - + +
172L ARG* 4.9 1.4 - - - +
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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