Contacts of the helix formed by residues 119 - 129 (chain A) in PDB entry 4I6N
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 ASP 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LEU* 1.3 75.9 - - - +
120A SER* 1.3 67.1 + - - +
121A ALA* 3.0 22.0 + - - +
122A SER* 3.0 16.2 + - - +
123A ARG* 3.0 18.5 + - - +
60C MSE 5.3 0.2 + - - -
62C LYS 4.6 1.8 + - - +
64C VAL* 3.7 21.2 - - + +
179C ARG* 3.4 28.6 - - - +
180C ALA* 2.9 22.6 + - - +
181C ALA* 3.3 31.7 + - - +
182C PRO 5.4 0.2 - - - +
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Residues in contact with SER 120 (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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76A PHE* 2.9 48.2 + - - +
78A GLN* 3.1 16.1 + - - -
118A LEU 3.6 1.8 + - - -
119A ASP* 1.3 76.3 + - - +
121A ALA* 1.3 57.2 + - - +
123A ARG* 3.2 15.0 + - - +
124A GLY 3.0 22.2 + - - -
180A ALA 4.0 2.3 + - - -
181A ALA* 5.6 0.2 - - - -
180C ALA* 3.8 15.7 - - - -
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Residues in contact with ALA 121 (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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-2A LEU* 3.7 20.1 - - + +
78A GLN* 3.5 25.8 - - - +
80A VAL* 3.8 7.0 - - + +
119A ASP* 3.0 14.6 + - - +
120A SER* 1.3 77.2 - - - +
122A SER* 1.3 63.6 + - - +
124A GLY* 3.2 2.4 + - - -
125A LEU 3.1 17.5 + - - -
78C GLN* 3.9 1.3 - - - +
178C LEU 3.9 20.6 - - - +
179C ARG* 4.4 0.7 - - - -
180C ALA* 3.9 5.4 - - - +
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2A LEU* 4.5 3.4 - - - -
118A LEU* 4.3 9.9 - - - -
119A ASP* 3.0 18.3 + - - +
121A ALA* 1.3 77.4 - - - +
123A ARG* 1.3 66.3 + - - +
125A LEU* 3.1 7.6 + - - +
126A CYS* 3.0 29.5 + - - -
301A DTT 5.1 0.2 - - - +
60C MSE 3.1 51.8 + - - +
179C ARG* 6.0 0.5 - - - +
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Residues in contact with ARG 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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74A VAL 4.6 6.1 + - - -
75A TYR* 3.7 29.4 - - - +
76A PHE* 2.7 47.7 + - - +
77A SER* 3.6 11.9 - - - -
111A PHE* 4.0 4.0 - - - -
115A THR* 2.8 40.2 + - - +
116A TYR 2.9 22.2 + - - -
117A ASP* 4.8 0.2 - - - +
118A LEU* 3.0 18.6 + - + +
119A ASP 3.0 16.8 + - - +
120A SER* 3.2 20.3 + - - +
122A SER* 1.3 74.8 - - - +
124A GLY* 1.3 63.9 + - - +
126A CYS* 3.3 4.1 + - - +
127A LEU* 3.0 22.9 + - - +
64C VAL* 5.6 2.0 - - - +
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Residues in contact with GLY 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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77A SER* 3.8 0.8 - - - -
78A GLN 3.1 26.5 - - - -
80A VAL* 4.2 2.9 - - - -
88A GLN* 3.5 14.5 + - - -
120A SER 3.0 10.9 + - - -
121A ALA 3.2 2.0 + - - -
122A SER 3.1 0.6 - - - -
123A ARG* 1.3 77.4 - - - +
125A LEU* 1.3 56.4 + - - +
127A LEU* 3.3 3.6 + - - +
128A THR* 2.8 32.7 + - - -
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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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-2A LEU* 3.8 26.0 - - + +
1A MSE 3.9 20.6 - - + -
2A ALA* 3.9 17.9 - - + +
80A VAL* 3.9 16.5 - - + +
121A ALA 3.1 13.3 + - - +
122A SER* 3.1 7.4 + - - +
124A GLY* 1.3 75.1 - - - +
126A CYS* 1.3 58.3 + - - +
128A THR* 3.2 1.3 + - - -
129A ASN* 2.9 44.9 + - - +
301A DTT 3.4 21.3 - - + +
60C MSE 3.3 30.5 - - - -
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Residues in contact with CYS 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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111A PHE* 4.0 17.0 - - + -
114A PHE* 3.9 12.1 - - + -
115A THR* 4.1 4.9 - - + -
118A LEU* 4.1 15.3 - - - -
122A SER* 3.0 24.0 + - - -
123A ARG 3.5 8.3 - - - +
125A LEU* 1.3 77.5 - - - +
127A LEU* 1.3 62.4 + - - +
129A ASN* 3.5 2.3 + - - +
130A SER* 3.2 22.0 + - - -
301A DTT 2.1 49.6 - - - -
60C MSE 5.9 0.7 - - - -
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Residues in contact with LEU 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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6A TRP* 3.8 28.1 - - + -
77A SER* 3.8 19.7 - - - +
84A ALA* 4.8 3.4 - - + -
87A SER* 4.8 0.9 - - - -
88A GLN* 4.0 37.0 - - - +
91A ILE* 4.0 36.1 - - + -
111A PHE* 3.8 17.6 - - + -
123A ARG 3.0 13.3 + - - +
124A GLY* 3.5 8.7 - - - +
126A CYS* 1.3 77.4 - - - +
128A THR* 1.3 66.9 + - - +
130A SER* 3.1 19.5 + - - -
133A ILE* 4.5 8.7 - - + +
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Residues in contact with THR 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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2A ALA* 3.9 23.6 - - + -
3A GLU 3.9 7.7 - - - +
4A GLY 5.8 0.2 - - - +
6A TRP* 3.2 42.0 + - - +
80A VAL* 3.1 20.1 + - + +
81A ILE* 3.8 23.7 - - + +
84A ALA* 4.9 1.0 - - - +
88A GLN* 4.5 7.4 + - - -
124A GLY 2.8 21.4 + - - -
125A LEU* 3.2 5.1 + - - -
127A LEU* 1.3 77.6 - - - +
129A ASN* 1.3 62.3 + - - +
130A SER 3.6 0.3 + - - -
134A ARG* 4.5 3.5 - - - -
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Residues in contact with ASN 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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1A MSE 2.9 23.1 + - - -
2A ALA* 3.4 3.6 - - - -
3A GLU* 2.7 38.2 + - + +
125A LEU* 2.9 21.7 + - - +
126A CYS 3.8 4.3 - - - +
127A LEU 3.2 0.2 - - - -
128A THR* 1.3 78.3 - - - +
130A SER* 1.3 62.3 + - - +
131A GLU* 3.3 10.4 + - - +
134A ARG* 6.2 0.4 - - - -
301A DTT 2.8 37.4 + - - +
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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