Contacts of the helix formed by residues 95 - 108 (chain A) in PDB entry 5CIV
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLY 4.0 5.8 + - - +
91A TYR* 3.6 18.4 - - + -
92A LYS* 2.8 51.0 + - + +
94A ASN* 1.3 84.7 - - + +
96A LEU* 1.3 63.5 + - - +
97A GLY 3.2 2.9 - - - +
98A GLY* 3.2 6.2 + - - +
99A LEU* 3.1 20.2 + - - +
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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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67A TRP* 4.0 22.0 - - + -
87A PRO* 4.6 5.2 - - + -
93A TRP* 3.3 46.4 - - + +
94A ASN 3.6 2.8 + - - -
95A GLN* 1.3 74.2 - - - +
97A GLY* 1.3 61.2 + - - +
99A LEU* 3.1 13.8 + - + +
100A TYR* 2.8 60.9 + - + +
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Residues in contact with GLY 97 (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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95A GLN* 3.2 1.2 - - - +
96A LEU* 1.3 78.9 - - - +
98A GLY* 1.3 60.6 + - - +
100A TYR* 3.4 10.7 + - - +
101A GLN* 3.2 28.1 + - - +
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Residues in contact with GLY 98 (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 TYR* 3.5 20.4 + - - -
95A GLN* 3.2 9.6 + - - +
97A GLY* 1.3 72.3 - - - +
99A LEU* 1.3 65.6 + - - +
101A GLN* 3.3 8.2 + - - +
102A SER* 3.0 18.7 + - - -
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Residues in contact with LEU 99 (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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67A TRP* 4.0 27.6 - - + -
70A LEU* 4.0 9.2 - - + -
87A PRO* 4.2 12.1 - - + -
88A ALA* 4.0 15.5 - - + -
91A TYR* 3.6 30.8 - - + -
95A GLN 3.1 13.8 + - - +
96A LEU* 3.5 17.9 - - + +
98A GLY* 1.3 76.6 - - - +
100A TYR* 1.3 63.4 + - + +
102A SER* 2.5 29.8 + - - +
103A PHE* 3.1 36.2 + - + -
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Residues in contact with TYR 100 (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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55A ARG* 6.2 1.1 - - - -
63A TYR* 3.6 33.6 + + + -
67A TRP* 3.3 36.8 - + - -
96A LEU* 2.8 53.8 + - + +
97A GLY* 3.7 8.7 - - - +
99A LEU* 1.3 77.8 - - + +
101A GLN* 1.3 62.8 + - - +
103A PHE* 3.0 25.6 + + - +
104A TYR* 3.0 37.4 + - + +
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Residues in contact with GLN 101 (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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55A ARG* 4.8 6.7 - - - +
59A GLU* 5.1 2.5 + - - +
97A GLY 3.2 15.5 + - - +
98A GLY* 3.6 10.5 - - - +
99A LEU 3.3 0.2 - - - -
100A TYR* 1.3 78.1 - - - +
102A SER* 1.3 58.1 + - - +
104A TYR* 3.3 34.4 + - - +
105A ALA* 2.9 30.0 + - - +
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Residues in contact with SER 102 (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 TYR* 3.5 28.3 - - - -
98A GLY 3.0 7.5 + - - -
99A LEU* 2.5 33.9 + - - +
101A GLN* 1.3 76.1 - - - +
103A PHE* 1.3 66.8 + - - +
105A ALA* 3.5 6.9 + - - +
106A ALA* 3.0 24.4 + - - +
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Residues in contact with PHE 103 (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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62A ALA* 3.8 13.6 - - - +
63A TYR* 4.0 12.8 - + - -
66A GLY* 3.5 35.9 - - - -
67A TRP* 3.7 33.7 - + - -
70A LEU* 4.1 13.7 - - + -
99A LEU* 3.1 42.0 + - + -
100A TYR* 3.0 27.4 + + - +
102A SER* 1.3 81.1 + - - +
104A TYR* 1.3 67.6 + - + +
106A ALA* 3.2 9.9 + - + -
107A TYR* 3.2 28.1 - + - -
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Residues in contact with TYR 104 (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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55A ARG* 3.2 39.4 + - - -
59A GLU* 3.6 52.0 - - + +
62A ALA* 4.0 11.3 - - + +
63A TYR* 3.9 21.2 - + + -
100A TYR* 3.0 35.9 + - + +
101A GLN* 3.5 38.8 - - - +
103A PHE* 1.3 78.8 - - + +
105A ALA* 1.3 63.4 + - - +
107A TYR 3.4 0.9 + - - -
108A ALA* 3.1 26.3 + - - +
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Residues in contact with ALA 105 (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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101A GLN 2.9 18.3 + - - +
102A SER* 3.8 7.4 - - - +
104A TYR* 1.3 77.2 - - - +
106A ALA* 1.3 62.3 + - - +
107A TYR 3.3 0.7 + - - -
108A ALA* 3.5 16.2 + - - +
109A ASP* 5.1 0.9 + - - +
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Residues in contact with ALA 106 (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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102A SER 3.0 17.5 + - - +
103A PHE* 3.2 8.0 + - - +
105A ALA* 1.3 76.1 - - - +
107A TYR* 1.3 80.7 + - + +
109A ASP* 3.7 9.9 - - - +
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Residues in contact with TYR 107 (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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46A LYS* 5.1 0.3 + - - -
62A ALA* 4.0 23.1 - - + -
65A LEU* 3.6 30.4 + - + +
66A GLY* 4.2 8.6 - - - -
69A HIS* 3.7 24.9 + - - +
103A PHE* 3.2 27.3 + + - +
104A TYR 3.8 1.1 - - - -
105A ALA 3.2 0.2 - - - -
106A ALA* 1.3 91.2 - - + +
108A ALA* 1.3 64.0 + - - +
109A ASP* 3.1 7.8 + - - -
110A LEU* 3.2 26.4 + - + +
115A LEU* 3.8 20.9 - - + +
118A LEU* 3.7 25.4 - - + -
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Residues in contact with ALA 108 (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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46A LYS* 2.9 30.5 + - - +
104A TYR 3.1 16.6 + - - +
105A ALA* 3.5 15.3 + - - +
106A ALA 3.6 0.2 - - - -
107A TYR* 1.3 77.4 - - - +
109A ASP* 1.3 57.5 + - - +
110A LEU 3.4 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