Contacts of the helix formed by residues 122 - 128 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1I MET* 4.3 2.0 - - + -
55K ARG* 4.4 0.2 - - - +
57K VAL* 5.0 3.6 - - + -
84K ALA* 4.1 30.5 - - + +
87K CYS* 3.9 14.1 - - + -
164K TYR* 5.1 1.8 - - - +
120N ASP 3.8 9.0 - - - +
121N ILE* 1.3 80.5 - - - +
123N PHE* 1.3 64.6 + - - +
124N ASP* 2.9 24.3 + - - +
125N GLU* 3.0 41.6 + - - +
126N LEU* 3.0 11.4 + - - +
209N VAL* 4.3 3.4 - - - -
213N ARG* 4.3 4.3 - - - +
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Residues in contact with PHE 123 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K CYS* 4.5 9.5 - - - -
89K GLY* 3.6 20.2 - - - +
90K ASP* 3.8 13.2 - - + -
166K ILE* 3.6 25.1 - - + -
167K GLY 3.4 23.1 - - - -
122N THR* 1.3 73.4 - - - +
124N ASP* 1.3 61.4 + - - +
126N LEU* 3.4 4.9 + - - +
127N TYR* 3.3 31.7 + + - -
203N HIS* 3.8 33.0 - + - -
205N LEU* 3.5 30.4 - - + +
206N ASN* 3.4 26.7 - - - -
209N VAL* 3.8 14.6 - - + +
213N ARG* 5.3 0.8 - - - +
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Residues in contact with ASP 124 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K CYS* 4.0 2.4 - - - -
111K VAL* 4.4 17.7 - - + +
132K TRP* 5.2 3.8 - - - -
134K LEU* 4.6 8.9 - - + +
164K TYR* 4.6 2.4 + - - -
166K ILE* 3.6 32.5 - - + +
225K GLY 5.2 3.1 - - - +
227K ILE* 3.9 25.8 - - + +
122N THR* 2.9 22.9 + - - +
123N PHE* 1.3 76.2 - - - +
125N GLU* 1.3 76.4 + - - +
127N TYR* 3.3 25.8 + - - +
128N ASN* 3.6 6.6 + - - +
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Residues in contact with GLU 125 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55K ARG* 3.3 30.1 + - - -
57K VAL* 4.3 6.9 - - - +
225K GLY 5.6 5.6 - - - +
114N ARG* 5.8 0.3 + - - -
118N ALA* 5.4 1.7 - - - +
121N ILE* 3.4 21.8 - - + +
122N THR* 3.0 39.5 + - - +
124N ASP* 1.3 84.2 - - - +
126N LEU* 1.3 65.2 + - - +
128N ASN* 3.3 16.4 + - - +
129N ALA* 3.6 9.9 + - - +
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Residues in contact with LEU 126 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N LEU* 4.7 2.0 - - + -
112N LEU* 5.2 7.4 - - + -
116N LEU* 4.2 23.8 - - + -
121N ILE* 4.1 12.0 - - + +
122N THR 3.0 11.4 + - - +
123N PHE 3.6 8.7 - - - +
124N ASP 3.3 0.2 - - - -
125N GLU* 1.3 75.6 - - - +
127N TYR* 1.3 66.0 + - - +
129N ALA* 2.8 19.4 + - + +
130N ILE* 3.4 11.5 + - + +
205N LEU* 3.7 37.7 - - + +
208N ALA* 3.5 46.2 - - + +
209N VAL* 4.1 8.5 - - + +
212N ALA* 4.4 3.1 - - + -
228N ILE* 5.6 0.9 - - + -
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Residues in contact with TYR 127 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K TRP* 4.3 14.4 - + + +
134K LEU* 3.8 17.7 - - + -
167K GLY 3.6 20.2 - - - -
168K GLY* 3.7 12.1 - - - -
169K PRO* 3.7 4.3 - - - +
170K ALA* 3.5 41.5 + - + -
123N PHE* 3.3 26.8 + + - -
124N ASP* 3.3 10.8 - - - +
125N GLU 3.3 0.2 - - - -
126N LEU* 1.3 80.1 - - - +
128N ASN* 1.3 61.0 + - - +
129N ALA 3.1 1.2 + - - -
130N ILE* 3.3 26.6 + - + +
173N PRO* 4.6 18.8 - - + +
176N LEU 4.8 1.4 + - - -
178N LEU* 4.3 19.2 + - + +
203N HIS* 4.5 7.1 + - - -
205N LEU* 3.6 25.6 - - + +
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Residues in contact with ASN 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K VAL* 6.2 1.1 - - + -
131K GLU* 2.9 32.9 + - - +
132K TRP* 2.6 41.4 - - + +
172K ARG* 4.5 2.6 - - - +
113N ASN* 2.6 25.3 + - - -
114N ARG* 3.1 33.0 + - - +
124N ASP 3.6 4.8 + - - +
125N GLU* 3.3 12.6 + - - +
126N LEU 3.1 1.0 - - - -
127N TYR* 1.3 78.7 - - - +
129N ALA* 1.3 49.0 + - - +
130N ILE 3.5 1.5 - - - +
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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