Contacts of the helix formed by residues 121 - 132 (chain A) in PDB entry 3HSJ
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 ARG 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ASP* 5.9 0.2 + - - -
115A HIS* 3.8 21.7 + - - -
116A TYR* 3.7 20.4 + - - -
117A ASP* 2.7 39.5 + - - +
118A MET 3.1 8.5 + - - +
119A LYS 3.4 1.2 + - - -
120A ASN* 1.3 79.9 - - + +
122A GLY* 1.3 66.9 + - - +
123A PHE* 3.1 41.9 - - + +
124A MET* 3.0 26.4 + - + +
125A LEU* 3.0 25.4 + - - +
152A PHE* 4.5 0.7 - - - -
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Residues in contact with GLY 122 (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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120A ASN 4.0 0.2 + - - -
121A ARG* 1.3 71.4 - - - +
123A PHE* 1.3 58.5 + - - +
125A LEU* 4.4 2.5 - - - -
126A TRP* 2.9 39.7 + - - +
152A PHE* 3.9 37.1 - - - -
153A ASP 5.3 0.2 - - - -
155A LEU* 3.9 8.7 - - - -
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Residues in contact with PHE 123 (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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42A THR* 3.5 40.4 - - + +
53A TYR* 4.3 9.4 - + - -
55A ALA* 3.6 17.6 - - + +
56A ALA 5.1 1.4 + - - +
121A ARG* 3.1 47.3 - - + -
122A GLY* 1.3 76.5 - - - +
124A MET* 1.3 74.1 + - + +
127A PRO* 3.2 21.1 - - - +
155A LEU* 3.7 14.0 - - + +
194A GOL 3.7 32.3 - - - -
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Residues in contact with MET 124 (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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6A ALA* 3.9 24.5 - - + -
57A ALA* 5.1 0.2 - - - +
97A ASP* 4.4 11.0 - - + +
99A MET* 3.8 27.3 - - + +
115A HIS* 3.9 28.7 - - + +
118A MET* 3.6 33.9 - - + +
121A ARG* 3.0 29.9 + - + +
123A PHE* 1.3 98.4 - - + +
125A LEU* 1.3 64.6 + - + +
126A TRP 3.5 0.2 - - - -
127A PRO* 3.5 3.4 - - - +
128A LEU* 3.3 23.5 + - - +
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Residues in contact with LEU 125 (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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118A MET* 3.3 42.2 - - + +
119A LYS* 3.7 17.0 - - + +
121A ARG 3.0 10.7 + - - +
122A GLY* 4.2 2.2 - - - +
124A MET* 1.3 74.4 - - - +
126A TRP* 1.3 61.3 + - - +
128A LEU* 3.3 5.3 + - + +
129A PHE* 2.8 30.5 + - - +
137A PHE* 4.4 5.8 - - + -
143A LEU* 3.8 20.9 - - + +
146A ILE* 3.8 16.6 - - + -
147A LEU* 3.8 17.5 - - + +
152A PHE* 3.6 32.1 - - + -
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Residues in contact with TRP 126 (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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40A TYR* 4.6 10.3 + - + -
122A GLY* 2.9 27.4 + - - +
125A LEU* 1.3 77.2 - - - +
127A PRO* 1.3 69.2 - - + +
129A PHE* 3.2 32.0 + + - +
130A GLU* 3.1 19.8 + - - +
147A LEU* 3.9 35.0 - - + +
151A ALA 5.9 0.2 - - - -
152A PHE* 3.2 23.1 + - + +
153A ASP 3.1 27.4 + - - -
154A LYS* 3.6 44.6 - - + -
155A LEU* 3.7 16.6 - - + +
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Residues in contact with PRO 127 (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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37A SER* 3.5 28.1 - - - +
40A TYR* 3.6 35.0 - - + -
55A ALA 4.4 2.2 - - - +
56A ALA* 4.0 6.5 - - - -
57A ALA* 3.8 15.7 - - + +
122A GLY 3.8 0.2 - - - +
123A PHE* 3.2 31.0 - - - +
124A MET 3.5 5.2 - - - +
126A TRP* 1.3 94.7 - - + +
128A LEU* 1.3 62.2 + - - +
130A GLU* 3.2 16.9 + - + +
131A ILE* 3.4 6.1 + - - +
155A LEU* 5.3 0.9 - - + -
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Residues in contact with LEU 128 (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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4A TYR* 3.4 46.2 - - + -
57A ALA* 3.8 6.0 - - - +
99A MET* 4.3 10.8 - - + -
100A LEU* 4.1 11.9 - - + -
118A MET* 3.7 29.8 - - + -
124A MET 3.3 17.1 + - - +
125A LEU* 3.6 4.9 - - + +
126A TRP 3.2 0.2 - - - -
127A PRO* 1.3 80.6 - - - +
129A PHE* 1.3 57.8 + - - +
131A ILE* 3.1 6.5 + - + +
132A ALA* 2.8 28.0 + - + -
135A LEU* 4.1 11.4 - - + -
137A PHE* 4.8 0.4 - - + -
143A LEU* 3.8 22.7 - - + -
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Residues in contact with PHE 129 (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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125A LEU 2.8 17.5 + - - +
126A TRP* 3.2 31.4 + + - +
128A LEU* 1.3 76.4 - - - +
130A GLU* 1.3 64.8 + - - +
132A ALA 4.3 0.9 - - - -
133A PRO* 3.2 56.7 - - + +
143A LEU* 3.6 15.8 - - + +
144A ARG* 4.2 18.8 - - + -
147A LEU* 3.5 20.9 - - + -
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Residues in contact with GLU 130 (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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37A SER* 3.5 4.7 - - - -
38A SER* 2.7 44.0 + - - -
40A TYR* 2.7 35.5 + - - +
126A TRP 3.1 8.2 + - - +
127A PRO 3.2 9.4 + - - +
129A PHE* 1.3 81.7 - - - +
131A ILE* 1.3 61.7 + - + +
133A PRO* 4.0 5.5 - - - +
157A LYS* 3.6 4.7 + - - -
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Residues in contact with ILE 131 (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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4A TYR* 4.0 17.9 - - + -
35A THR* 3.8 19.8 - - + +
36A VAL 3.8 5.4 - - - +
37A SER* 3.5 33.0 - - - +
57A ALA* 3.8 30.3 - - + +
58A VAL 4.0 1.3 - - - -
59A ALA* 3.8 24.7 - - + +
127A PRO 3.4 5.1 + - - +
128A LEU* 3.1 13.2 + - - +
130A GLU* 1.3 81.5 - - + +
132A ALA* 1.3 58.1 + - - +
133A PRO* 3.6 5.3 - - - +
191A ACT 4.5 0.2 - - - +
195A GOL 2.8 24.8 + - - -
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Residues in contact with ALA 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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4A TYR* 3.5 28.0 - - + +
128A LEU* 2.8 12.3 + - + +
129A PHE 3.7 2.7 - - - -
131A ILE* 1.3 80.8 - - - +
133A PRO* 1.3 66.5 - - - +
134A GLU 3.1 3.4 - - - -
135A LEU* 3.1 27.5 + - + +
143A LEU* 3.7 9.0 - - - +
191A ACT 3.3 18.8 - - - +
195A GOL 3.8 0.2 - - - +
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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