Contacts of the helix formed by residues 131 - 143 (chain A) in PDB entry 4HYY
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 GLY 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A THR* 1.3 80.1 - - - +
132A LYS* 1.3 64.8 + - - +
133A THR 3.2 1.8 - - - -
134A GLN* 3.8 17.3 - - - -
135A LEU* 2.7 27.4 + - - +
303A LEU* 4.1 8.1 - - - -
311A ARG* 3.7 7.5 - - - +
328A PHE* 4.8 13.4 - - - -
330A ILE* 4.8 5.6 - - - -
335A ILE* 4.9 0.2 - - - -
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Residues in contact with LYS 132 (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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124A ALA* 4.1 16.2 - - - +
126A GLY* 3.5 19.8 + - - +
127A GLU 3.3 27.9 + - - -
128A PHE* 4.6 4.9 - - - +
129A ARG 5.5 0.4 - - - +
130A THR 2.6 18.0 + - - +
131A GLY* 1.3 74.2 - - - +
133A THR* 1.3 58.7 + - - +
135A LEU* 3.4 5.2 + - - +
136A SER* 2.9 26.8 + - - -
223A ASP* 5.2 0.7 - - - +
265A PHE* 4.3 0.5 - - - -
267A THR* 3.8 25.0 - - + +
268A ASN 3.6 24.1 + - - +
269A GLN* 4.7 16.1 - - - +
303A LEU* 3.9 18.0 - - + +
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Residues in contact with THR 133 (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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130A THR 4.1 2.6 + - - -
131A GLY 3.2 0.2 - - - -
132A LYS* 1.3 77.0 - - - +
134A GLN* 1.3 63.5 + - + +
135A LEU 3.2 1.8 - - - -
136A SER* 3.1 7.5 + - - -
137A HIS* 2.9 57.6 + - + +
162A GLU* 6.0 0.2 - - - +
164A THR* 4.1 19.1 + - - +
223A ASP* 3.2 25.3 + - - +
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Residues in contact with GLN 134 (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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130A THR 5.2 0.6 + - - +
131A GLY* 3.1 12.7 + - - +
133A THR* 1.3 81.5 - - + +
135A LEU* 1.3 54.5 + - - +
137A HIS* 3.4 6.1 + - - +
138A THR* 2.7 36.4 + - - -
169A ARG* 2.5 44.1 + - - +
173A ILE* 5.1 0.3 - - - +
330A ILE* 4.2 22.5 - - + +
331A THR 3.8 10.7 + - - -
334A GLY* 4.3 10.1 - - - -
335A ILE* 3.4 16.4 - - + -
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Residues in contact with LEU 135 (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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103A THR* 4.2 26.0 - - + +
108A PHE* 3.9 29.4 - - + -
116A ILE* 5.2 4.5 - - + -
124A ALA* 4.6 9.4 - - + -
131A GLY 2.7 21.3 + - - +
132A LYS 3.5 4.5 - - - +
134A GLN* 1.3 71.8 - - - +
136A SER* 1.3 66.0 + - - +
138A THR* 3.1 2.6 + - - -
139A LEU* 3.0 54.6 + - + +
265A PHE* 3.6 27.8 - - + -
301A ILE* 5.5 0.7 - - + -
303A LEU* 5.2 4.5 - - + -
328A PHE* 6.2 0.7 - - + -
335A ILE* 3.4 14.1 - - + +
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Residues in contact with SER 136 (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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132A LYS 2.9 16.6 + - - -
133A THR* 3.1 11.5 + - - -
135A LEU* 1.3 79.0 - - - +
137A HIS* 1.3 63.2 + - - +
139A LEU* 3.3 0.9 + - - -
140A CYS* 3.3 24.4 + - - -
158A PHE* 4.0 24.2 - - - -
221A ILE* 3.6 13.0 - - - +
223A ASP* 4.2 5.1 - - - -
265A PHE* 3.4 22.0 - - - -
267A THR* 3.7 10.0 - - - +
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Residues in contact with HIS 137 (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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133A THR* 2.9 48.8 + - + +
134A GLN* 4.0 7.2 + - - +
136A SER* 1.3 78.0 - - - +
138A THR* 1.3 64.0 + - - +
140A CYS* 3.1 21.0 + - - +
141A VAL* 3.7 2.1 + - - +
158A PHE* 5.3 4.9 - + - -
164A THR 3.6 13.7 - - - -
165A PHE* 3.6 16.7 - + - -
166A ARG* 3.0 44.5 + - + +
169A ARG* 3.8 17.7 - - + +
170A LEU* 3.4 26.2 - - + +
173A ILE* 3.9 14.9 - - + +
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Residues in contact with THR 138 (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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103A THR 3.3 26.9 - - - +
104A GLY* 4.9 0.9 - - - -
134A GLN 2.7 21.0 + - - -
135A LEU* 3.1 8.2 + - + -
137A HIS* 1.3 78.6 - - - +
139A LEU* 1.3 57.8 + - - +
141A VAL* 2.8 22.7 + - - +
142A THR* 2.9 25.3 + - + +
173A ILE* 4.1 15.6 - - + +
176A ARG* 4.9 3.1 - - - +
177A PHE* 4.9 0.2 - - + -
334A GLY* 3.4 8.6 - - - -
335A ILE* 3.0 28.1 + - - +
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Residues in contact with LEU 139 (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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101A ILE* 4.1 7.9 - - + -
102A THR 3.5 24.0 - - - +
103A THR* 4.2 2.9 - - - -
116A ILE* 3.8 26.0 - - + -
135A LEU* 3.0 38.8 + - + +
136A SER* 3.9 3.8 - - - +
138A THR* 1.3 71.7 - - - +
140A CYS* 1.3 62.2 + - - +
141A VAL 2.9 5.4 - - - -
142A THR* 3.4 6.3 - - - +
143A ALA* 2.9 29.2 + - - +
219A LEU* 3.7 19.7 - - + -
221A ILE* 4.3 0.9 - - + -
265A PHE* 3.7 40.2 - - + -
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Residues in contact with CYS 140 (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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136A SER 3.3 14.8 + - - -
137A HIS* 3.1 14.6 + - - +
139A LEU* 1.3 76.0 - - - +
141A VAL* 1.3 58.0 + - - +
144A GLN* 2.9 30.5 + - - +
156A ILE* 3.4 14.1 - - - +
158A PHE* 3.5 31.9 - - - -
165A PHE* 4.0 14.6 - - - -
170A LEU* 3.8 19.3 - - + -
184A VAL* 5.0 0.2 - - - -
188A VAL* 3.9 14.3 - - + +
221A ILE* 4.0 6.0 - - - +
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Residues in contact with VAL 141 (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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137A HIS 4.2 5.2 - - - +
138A THR 2.8 9.6 + - - +
140A CYS* 1.3 82.7 - - - +
142A THR* 1.3 60.0 + - - +
143A ALA 3.1 2.0 - - - -
144A GLN* 2.8 28.4 + - - +
145A LEU* 3.5 13.8 + - + +
170A LEU* 4.2 14.1 - - + +
173A ILE* 3.6 25.8 - - + -
174A ALA* 4.4 11.9 - - - +
177A PHE* 3.9 26.5 - - + -
179A VAL* 5.2 1.3 - - + -
184A VAL* 3.8 27.4 - - + -
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Residues in contact with THR 142 (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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101A ILE* 3.6 7.2 - - - +
102A THR* 2.9 44.4 + - + +
104A GLY 4.6 3.6 - - - +
138A THR* 2.9 18.2 + - + +
139A LEU* 3.4 17.0 - - - +
141A VAL* 1.3 75.7 - - - +
143A ALA* 1.3 63.4 + - - +
144A GLN 3.0 0.4 - - - -
145A LEU* 3.1 29.2 + - + +
151A TYR* 4.3 2.8 - - - -
177A PHE* 3.5 35.7 - - + -
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Residues in contact with ALA 143 (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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101A ILE* 3.5 31.4 - - + +
139A LEU 2.9 19.3 + - - +
142A THR* 1.3 80.9 + - - +
144A GLN* 1.3 56.4 + - - +
151A TYR* 2.6 23.8 + - - +
153A GLY* 3.4 2.4 - - - -
154A GLY 3.0 16.1 + - - +
156A ILE* 3.6 22.7 - - + -
218A LYS* 5.1 1.8 - - + -
219A LEU* 3.9 6.3 - - + -
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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