Contacts of the helix formed by residues 82 - 92 (chain A) in PDB entry 4J1O
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 GLN 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ASN* 3.5 39.6 + - - +
80A PRO 3.2 2.9 - - - -
81A LEU* 1.3 83.6 - - + +
83A PRO* 1.3 61.6 - - - +
84A LEU 3.2 0.5 + - - -
85A VAL* 3.8 22.3 - - + +
86A LEU* 2.8 29.9 + - - +
122B ASP* 2.9 33.0 + - - +
125B GLY 3.2 14.1 - - - +
126B GLY* 3.8 5.6 - - - -
127B VAL* 3.6 19.8 + - - +
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Residues in contact with PRO 83 (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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80A PRO 5.4 1.3 - - - +
81A LEU 3.6 9.2 - - - +
82A GLN* 1.3 87.1 - - - +
84A LEU* 1.3 56.5 + - - +
86A LEU* 3.7 9.5 - - + +
87A ARG* 3.0 26.9 + - - +
90A MET* 5.9 0.2 - - - +
105A ASP* 4.9 4.9 - - - +
108A ALA* 5.7 3.4 - - + -
109A TYR* 3.4 50.0 - - + +
112A MET* 3.8 15.0 - - + -
274A GLN* 4.3 10.3 - - + +
122B ASP 4.9 2.2 - - - +
125B GLY* 3.6 17.0 - - - +
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Residues in contact with LEU 84 (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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83A PRO* 1.3 76.2 - - - +
85A VAL* 1.3 67.8 + - + +
87A ARG* 3.2 37.0 + - - +
88A ARG* 3.1 55.6 + - + +
274A GLN* 3.9 17.4 - - - +
124B LEU 4.8 0.7 - - - +
125B GLY* 2.9 21.3 + - - +
126B GLY 5.8 0.4 - - - +
280B ARG* 3.5 41.1 - - - +
281B ASP* 4.1 2.9 - - - +
284B GLU* 4.2 2.0 - - - +
311B THR* 4.0 6.3 - - - +
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Residues in contact with VAL 85 (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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79A ASN 6.0 0.4 - - - +
82A GLN* 3.2 25.0 + - + +
84A LEU* 1.3 75.0 - - + +
86A LEU* 1.3 65.1 + - - +
88A ARG* 3.3 15.9 + - + +
89A ARG* 3.0 24.5 + - + +
125B GLY 3.4 0.8 + - - +
126B GLY* 3.7 25.4 - - - +
127B VAL 3.6 25.4 - - - +
128B ALA* 4.2 7.6 - - - +
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Residues in contact with LEU 86 (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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3A ILE* 4.5 10.8 - - + -
37A ILE* 5.4 0.2 - - + -
75A LEU* 4.2 16.2 - - + -
78A ALA* 3.9 28.7 - - + -
79A ASN 4.5 8.3 + - - +
80A PRO* 4.6 8.5 - - + +
82A GLN 2.8 18.5 + - - +
83A PRO* 3.7 7.4 - - + +
85A VAL* 1.3 78.9 - - - +
87A ARG* 1.3 61.7 + - - +
89A ARG* 3.2 7.7 + - + +
90A MET* 3.0 27.1 + - + +
104A ILE* 4.0 24.7 - - + +
105A ASP* 5.2 2.5 - - - -
108A ALA* 3.6 30.7 - - + -
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Residues in contact with ARG 87 (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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83A PRO 3.0 17.8 + - - +
84A LEU* 3.2 27.0 + - - +
86A LEU* 1.3 76.8 - - - +
88A ARG* 1.3 59.7 + - - +
90A MET* 3.2 20.7 + - + +
91A ASP* 2.9 52.2 + - - +
101A LYS* 5.6 4.7 - - + -
105A ASP* 5.6 3.4 - - - +
271A GLY* 5.0 9.0 - - - +
274A GLN* 3.1 21.2 + - + +
275A GLN* 3.4 39.6 - - - +
281B ASP* 5.4 2.0 + - - +
284B GLU* 4.1 21.8 + - - +
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Residues in contact with ARG 88 (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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84A LEU* 3.1 40.1 + - + +
85A VAL* 3.7 17.0 - - - +
87A ARG* 1.3 78.4 - - - +
89A ARG* 1.3 62.6 + - - +
91A ASP* 3.2 13.8 + - - +
92A GLY* 3.0 19.4 + - - -
126B GLY 5.5 0.2 + - - -
128B ALA* 3.7 21.2 - - - +
280B ARG* 4.8 0.4 - - - +
284B GLU* 2.8 42.2 + - - +
311B THR 2.9 27.9 + - - -
312B VAL* 4.2 0.8 - - - +
313B GLN* 3.4 35.0 - - - +
314B PRO* 5.2 1.3 - - - +
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Residues in contact with ARG 89 (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 GLY 2.8 27.9 + - - +
75A LEU* 4.0 11.8 - - + +
76A ILE 3.4 22.0 + - - -
77A GLY 4.5 2.8 + - - -
78A ALA* 3.6 37.8 - - - +
85A VAL* 3.0 16.5 + - + +
86A LEU* 3.2 11.6 + - - +
88A ARG* 1.3 75.2 - - - +
90A MET* 1.3 63.2 + - - +
92A GLY* 3.1 11.8 + - - -
93A LEU* 3.4 20.7 + - + +
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Residues in contact with MET 90 (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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71A MET* 4.0 19.1 - - - +
75A LEU* 3.9 18.2 - - + -
86A LEU* 3.0 16.5 + - + +
87A ARG* 3.2 28.5 + - + +
89A ARG* 1.3 76.8 - - - +
91A ASP* 1.3 56.8 + - - +
93A LEU* 2.9 23.7 + - - +
94A LEU 3.0 14.4 + - - +
101A LYS* 3.6 48.6 - - + +
104A ILE* 3.6 37.0 - - + -
105A ASP* 4.4 10.1 - - + +
271A GLY 5.7 0.7 - - - +
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Residues in contact with ASP 91 (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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87A ARG* 2.9 44.6 + - - +
88A ARG* 3.2 14.7 + - - +
90A MET* 1.3 75.8 - - - +
92A GLY* 1.3 61.7 + - - +
93A LEU 3.1 1.1 + - - -
94A LEU 3.6 17.8 + - - +
95A CYS* 4.5 3.0 + - - +
98A ASN* 5.6 0.3 - - - +
101A LYS* 2.8 30.8 + - - +
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Residues in contact with GLY 92 (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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88A ARG 3.0 12.7 + - - -
89A ARG* 3.1 8.4 + - - -
91A ASP* 1.3 77.2 - - - +
93A LEU* 1.3 62.8 + - - +
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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