Contacts of the helix formed by residues 85 - 96 (chain A) in PDB entry 2C47
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLU* 3.0 10.3 + - - +
83A ALA* 3.5 26.2 + - - +
84A PRO* 1.3 75.6 - - - +
86A LEU* 1.3 66.1 + - - +
87A HIS* 3.3 3.1 - - - -
88A LEU* 3.0 28.3 + - + +
89A GLU* 3.2 11.5 + - - +
190A GLY* 6.1 1.3 - - - +
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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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75A LYS* 3.7 52.5 - - + +
76A LEU 5.5 0.2 - - - -
77A GLU* 3.4 32.2 + - + +
85A GLN* 1.3 76.8 - - - +
87A HIS* 1.3 57.7 + - - +
89A GLU* 3.2 15.8 + - - +
90A TYR* 2.9 27.4 + - - +
108A PHE* 3.7 22.4 - - + -
115A ASN* 3.8 17.9 - - + +
117A MET* 3.9 21.3 - - + +
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Residues in contact with HIS 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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77A GLU* 4.9 0.7 - - - -
84A PRO* 2.7 48.4 + - + +
86A LEU* 1.3 78.5 - - - +
88A LEU* 1.3 87.0 + - + +
90A TYR* 3.3 6.5 - - + +
91A ARG* 3.1 47.7 + - - +
108A PHE* 3.5 32.6 - + + -
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Residues in contact with LEU 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 PRO 4.2 11.7 - - - +
85A GLN* 3.0 20.3 + - + +
87A HIS* 1.3 102.6 - - + +
89A GLU* 1.3 64.7 + - - +
91A ARG* 3.1 44.1 - - - +
92A PHE* 3.2 23.4 + - + -
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Residues in contact with GLU 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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75A LYS* 2.8 38.1 + - - +
85A GLN 3.2 7.6 + - - +
86A LEU* 3.2 17.9 + - - +
88A LEU* 1.3 74.7 - - - +
90A TYR* 1.3 66.3 + - - +
92A PHE* 3.2 11.9 + - - +
93A TYR* 3.0 44.6 + - + -
117A MET* 4.8 2.7 - - - -
188A ASP* 3.5 8.3 - - - -
189A PHE* 3.2 36.3 + - + +
190A GLY* 4.0 11.3 + - - +
1300A 5ID 6.0 0.7 - - - +
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Residues in contact with TYR 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 LEU 2.9 13.1 + - - +
87A HIS* 3.3 12.6 - - - +
89A GLU* 1.3 75.5 - - - +
91A ARG* 1.3 67.6 + - + +
93A TYR* 3.2 2.9 + - - +
94A LYS* 3.1 30.9 + - + +
105A VAL* 3.7 26.3 - - + +
106A TYR 6.0 0.3 - - - -
107A TYR* 4.6 3.9 - - - -
108A PHE* 3.7 49.7 + + + -
117A MET* 3.6 26.3 - - + -
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Residues in contact with ARG 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 HIS* 3.1 33.9 + - - +
88A LEU* 3.1 34.0 - - - +
90A TYR* 1.3 86.0 - - + +
92A PHE* 1.3 60.5 + - + +
94A LYS* 3.3 6.8 + - - +
95A GLN* 2.9 32.7 + - - +
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Residues in contact with PHE 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 LEU* 3.2 22.1 + - + -
89A GLU* 3.2 8.9 + - - +
91A ARG* 1.3 80.5 - - + +
93A TYR* 1.3 65.5 + - - +
94A LYS 3.1 0.2 + - - -
95A GLN* 3.2 16.7 + - - +
96A LEU* 3.1 26.9 + - - +
161A LEU* 3.4 40.4 - - + -
189A PHE* 3.4 36.8 - - + -
190A GLY 5.6 0.7 - - - -
192A ALA* 3.5 37.0 - - + -
193A LYS* 4.0 4.7 - - - -
194A GLU* 4.5 7.6 - - + -
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Residues in contact with TYR 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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75A LYS* 6.4 0.2 - - + -
89A GLU* 3.0 42.4 + - + -
90A TYR 3.7 5.6 - - - +
92A PHE* 1.3 75.6 - - - +
94A LYS* 1.3 57.9 + - - +
96A LEU* 3.2 9.2 + - - +
97A SER* 3.0 25.3 + - - -
102A VAL* 4.6 8.5 - - + +
103A PRO* 3.6 38.8 - - + +
105A VAL* 3.6 22.2 - - + +
117A MET* 3.1 26.9 - - + -
119A LEU* 3.9 18.0 - - + +
186A ILE 4.5 0.2 - - - -
187A ILE* 3.7 7.8 - - - +
188A ASP* 3.0 24.3 + - - -
189A PHE* 3.7 27.6 - + - -
1300A 5ID 4.1 3.6 - - - +
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Residues in contact with LYS 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 TYR* 3.1 27.8 + - + +
91A ARG* 3.6 9.9 - - - +
93A TYR* 1.3 73.6 - - - +
95A GLN* 1.3 66.0 + - - +
96A LEU 3.1 1.6 - - - -
97A SER* 2.7 27.7 + - - +
105A VAL* 5.0 4.2 - - + +
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Residues in contact with GLN 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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91A ARG* 2.9 13.5 + - - +
92A PHE* 3.4 25.6 - - - +
94A LYS* 1.3 77.3 - - - +
96A LEU* 1.3 58.4 + - + +
97A SER 3.7 0.3 + - - -
98A ALA* 5.2 0.3 + - - +
159A LYS* 3.1 48.6 - - + +
160A SER* 4.7 1.6 - - - -
161A LEU* 3.7 28.4 - - + +
194A GLU* 4.0 19.8 + - - +
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Residues in contact with LEU 96 (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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92A PHE 3.1 15.8 + - - +
93A TYR* 3.2 8.9 + - - +
94A LYS 3.1 0.8 - - - -
95A GLN* 1.3 76.5 - - - +
97A SER* 1.3 65.4 + - - +
98A ALA 3.1 4.5 + - - -
99A THR* 3.5 9.5 + - - +
102A VAL* 3.4 28.2 - - + +
155A TYR* 3.8 15.7 + - + -
156A VAL* 4.0 22.9 - - + -
159A LYS* 3.9 24.5 - - + -
161A LEU* 4.0 12.8 - - + -
189A PHE* 3.3 48.2 - - + -
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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