Contacts of the helix formed by residues 84 - 95 (chain A) in PDB entry 3Q2K
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 LEU 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A THR* 4.1 7.4 - - - +
81A PRO* 3.0 27.5 + - + +
83A GLY* 1.3 77.4 - - - +
85A HIS* 1.3 65.0 + - - +
86A PRO 3.3 1.7 - - - -
87A TRP* 3.4 12.2 + - + +
88A GLN* 3.1 34.3 + - + +
180A TRP* 3.8 29.0 - - + -
500A NAI 3.4 47.8 - - + +
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Residues in contact with HIS 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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78A LEU* 3.5 26.6 + - + +
80A THR* 2.8 37.0 + - - -
81A PRO 3.6 4.5 - - - -
82A SER* 2.9 15.9 + - - -
84A LEU* 1.3 76.8 - - - +
86A PRO* 1.3 64.7 - - + +
88A GLN* 4.6 0.7 - - - +
89A ALA* 3.0 26.2 + - - +
101A SER* 3.2 21.5 + - - +
102A GLU* 3.5 17.4 - - + +
104A PRO 2.8 27.3 + - - -
105A MET 3.4 11.4 - - - +
115A MET* 3.9 0.6 - - - +
500A NAI 3.0 20.4 + - - -
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Residues in contact with PRO 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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82A SER 3.6 5.6 - - - +
83A GLY* 3.3 19.3 - - - +
85A HIS* 1.3 93.5 - - + +
87A TRP* 1.3 70.3 + - + +
89A ALA* 3.4 1.4 + - - +
90A ILE* 3.1 31.8 + - + +
105A MET 3.8 6.5 - - - +
106A ALA* 3.8 8.1 - - + -
107A THR 5.2 0.2 - - - +
111A ASP* 3.7 38.6 - - + +
114A ARG* 6.3 0.4 - - - -
115A MET* 3.6 23.1 - - + +
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Residues in contact with TRP 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 GLY 3.5 22.3 + - - -
84A LEU* 3.4 13.8 + - + +
86A PRO* 1.3 76.0 - - + +
88A GLN* 1.3 63.5 + - + +
90A ILE* 3.4 14.1 + - + +
91A GLU* 3.0 23.4 + - - +
111A ASP* 3.5 35.2 + - - -
114A ARG* 3.9 33.0 - - - -
180A TRP* 5.8 2.5 - + - -
117D LYS* 5.4 15.3 - - + -
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Residues in contact with GLN 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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16A VAL* 3.8 11.3 - - - +
64A LEU* 3.8 23.0 - - + +
78A LEU* 3.9 25.1 - - + +
80A THR* 2.9 30.2 + - - +
84A LEU* 3.1 27.4 + - + +
87A TRP* 1.3 77.5 - - + +
89A ALA* 1.3 57.1 + - - +
91A GLU* 3.2 4.9 + - - +
92A VAL* 2.8 35.1 + - - +
500A NAI 3.5 33.6 + - - -
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Residues in contact with ALA 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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78A LEU* 3.7 6.6 - - - +
85A HIS 3.0 21.1 + - - +
86A PRO 3.8 2.2 - - - +
87A TRP 3.3 0.4 - - - -
88A GLN* 1.3 75.9 - - - +
90A ILE* 1.3 58.7 + - - +
92A VAL* 3.7 1.5 - - - +
93A ALA* 2.8 29.8 + - - +
99A VAL* 3.9 27.8 - - + +
115A MET* 3.8 26.9 - - + -
119A CYS* 4.5 6.1 - - - -
126A LEU* 5.2 0.4 - - + -
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Residues in contact with ILE 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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86A PRO* 3.1 21.1 + - + +
87A TRP* 3.7 20.4 - - + +
89A ALA* 1.3 77.9 - - - +
91A GLU* 1.3 56.2 + - - +
93A ALA* 3.7 1.0 - - - +
94A GLN* 3.0 59.7 + - - +
114A ARG* 3.3 38.4 - - + +
115A MET* 4.0 12.3 - - - +
118A ALA* 3.8 30.1 - - + -
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Residues in contact with GLU 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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64A LEU* 3.7 21.1 - - + +
65A SER* 3.2 31.2 + - - -
68A LEU* 3.6 18.3 - - + +
87A TRP 3.0 15.6 + - - +
88A GLN* 3.7 9.1 - - - +
90A ILE* 1.3 75.8 - - - +
92A VAL* 1.3 62.4 + - - +
94A GLN* 3.3 16.7 + - - +
95A ALA* 3.3 16.1 + - - +
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Residues in contact with VAL 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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64A LEU* 4.3 8.5 - - + -
68A LEU* 3.9 11.7 - - + -
76A LEU* 3.1 41.7 - - + -
78A LEU* 4.7 7.9 - - + -
88A GLN 2.8 23.0 + - - +
89A ALA* 3.7 4.9 - - - +
91A GLU* 1.3 75.9 - - - +
93A ALA* 1.3 63.3 + - - +
95A ALA* 3.1 11.6 + - - +
96A GLY 3.4 0.2 + - - -
97A ARG* 3.3 34.4 + - + +
98A HIS 3.7 8.3 - - - +
99A VAL* 3.7 15.0 - - + -
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Residues in contact with ALA 93 (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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89A ALA 2.8 18.6 + - - +
90A ILE* 3.7 6.1 - - - +
92A VAL* 1.3 71.0 - - - +
94A GLN* 1.3 57.7 + - + +
95A ALA 3.0 4.7 - - - -
96A GLY* 2.9 17.2 + - - -
97A ARG 4.0 10.5 - - - -
99A VAL* 5.1 0.2 - - - -
118A ALA* 4.0 26.0 - - + +
119A CYS* 4.0 18.8 - - - -
122A ALA* 3.2 23.7 - - + +
124A VAL* 4.8 1.7 - - + +
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Residues in contact with GLN 94 (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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90A ILE* 3.0 41.0 + - + +
91A GLU* 3.5 16.8 - - - +
92A VAL 3.3 0.2 - - - -
93A ALA* 1.3 75.8 - - + +
95A ALA* 1.3 57.1 + - - +
96A GLY 3.2 1.1 - - - -
118A ALA* 5.6 3.1 - - + +
122A ALA* 5.3 1.3 - - - -
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Residues in contact with ALA 95 (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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68A LEU* 4.0 31.4 - - + +
91A GLU 3.3 9.7 + - - +
92A VAL 3.1 9.9 + - - +
93A ALA 3.0 1.4 - - - -
94A GLN* 1.3 77.0 - - - +
96A GLY* 1.3 58.5 + - - +
97A ARG* 3.1 24.4 + - - +
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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