Contacts of the helix formed by residues 94 - 105 (chain A) in PDB entry 3ROT
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 PHE 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A VAL* 3.7 16.6 - - + -
69A GLN* 3.2 47.8 - - + -
70A VAL* 3.6 18.2 - - + -
73A ILE* 3.5 20.6 - - + -
87A THR 4.9 1.6 - - - -
88A ILE* 3.8 22.4 - - + -
89A PRO* 3.5 22.2 - - + -
90A SER* 3.8 23.3 + - - -
92A THR 3.2 1.0 - - - -
93A ALA* 1.3 80.0 - - + +
95A SER* 1.3 65.2 + - - +
96A LYS 3.4 2.2 - - - -
97A SER* 3.1 8.8 + - - -
98A LEU* 2.8 41.5 + - + +
121A ASN* 3.9 2.6 - - - +
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Residues in contact with SER 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 ASP 3.6 7.3 + - - -
92A THR* 3.3 16.6 + - - -
93A ALA 3.6 0.2 - - - -
94A PHE* 1.3 74.4 - - - +
96A LYS* 1.3 59.0 + - - +
98A LEU* 3.2 2.8 + - - +
99A GLN* 2.8 40.4 + - - +
120A LYS* 3.6 18.2 + - - +
121A ASN* 2.6 31.2 + - - +
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Residues in contact with LYS 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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74A GLU* 5.1 2.7 - - - +
92A THR 5.0 0.4 + - - -
93A ALA 5.1 1.9 + - - +
94A PHE 3.4 0.8 - - - -
95A SER* 1.3 79.5 - - - +
97A SER* 1.3 59.0 + - - +
99A GLN* 3.3 16.3 + - - +
100A ARG* 2.8 31.3 + - + +
103A LYS* 5.4 0.3 + - - -
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Residues in contact with SER 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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70A VAL* 3.7 20.1 + - - +
73A ILE* 3.9 28.9 - - - +
74A GLU* 2.7 31.8 + - - -
77A LEU* 3.6 4.0 - - - +
93A ALA 4.8 0.7 + - - -
94A PHE* 3.1 13.3 + - - -
96A LYS* 1.3 77.7 - - - +
98A LEU* 1.3 57.6 + - - +
100A ARG* 3.3 3.9 + - - +
101A ALA* 2.9 30.2 + - - +
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Residues in contact with LEU 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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73A ILE* 5.8 6.1 - - + -
86A THR* 4.9 5.6 - - + -
88A ILE* 4.0 25.8 - - + -
94A PHE* 2.8 30.3 + - + +
95A SER 3.5 3.6 - - - +
97A SER* 1.3 73.8 - - - +
99A GLN* 1.3 62.5 + - - +
101A ALA* 3.3 6.2 + - + +
102A ASN* 2.9 28.2 + - - +
108A VAL* 4.1 25.0 - - + +
121A ASN* 3.4 40.8 - - + +
122A PRO* 3.4 29.3 - - + +
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Residues in contact with GLN 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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95A SER* 2.8 25.3 + - - +
96A LYS* 3.7 15.9 - - + +
98A LEU* 1.3 73.4 - - - +
100A ARG* 1.3 67.8 + - - +
102A ASN* 3.1 5.7 + - - +
103A LYS* 3.0 36.1 + - + +
119A THR 4.8 2.6 + - - +
120A LYS* 3.0 27.9 + - - +
122A PRO* 3.9 20.2 - - + -
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Residues in contact with ARG 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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74A GLU* 2.5 59.4 + - - +
77A LEU* 3.5 13.9 - - + +
78A ALA* 3.8 29.7 - - - +
96A LYS* 2.8 19.2 + - + +
97A SER* 3.4 4.7 - - - +
99A GLN* 1.3 76.7 - - - +
101A ALA* 1.3 64.6 + - - +
103A LYS* 2.9 30.4 + - - +
104A LEU* 3.0 31.1 + - + +
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Residues in contact with ALA 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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73A ILE* 5.9 1.1 - - + -
77A LEU* 3.5 29.3 - - + +
97A SER 2.9 14.2 + - - +
98A LEU* 3.5 10.1 - - + +
100A ARG* 1.3 76.1 - - - +
102A ASN* 1.3 63.1 + - - +
104A LEU* 3.2 5.2 + - - +
105A ASN 3.1 4.2 + - - -
106A ILE* 3.1 28.7 + - - +
108A VAL* 3.7 26.2 - - + -
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Residues in contact with ASN 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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98A LEU 2.9 13.7 + - - +
99A GLN* 3.3 10.9 + - - +
101A ALA* 1.3 77.9 - - - +
103A LYS* 1.3 63.3 + - - +
105A ASN* 3.2 13.7 + - - +
106A ILE 5.0 3.1 - - - -
122A PRO* 4.1 24.0 - - + +
124A LEU* 6.2 0.5 - - - +
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Residues in contact with LYS 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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96A LYS 5.4 0.2 + - - -
99A GLN* 3.0 29.4 + - + +
100A ARG* 2.9 21.7 + - - +
102A ASN* 1.3 76.0 - - + +
104A LEU* 1.3 63.7 + - + +
105A ASN* 3.1 8.5 + - - +
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Residues in contact with LEU 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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77A LEU* 4.3 11.2 - - + +
80A TYR* 3.8 38.7 - - + +
100A ARG* 3.0 42.6 + - + +
101A ALA* 3.2 6.5 + - - +
103A LYS* 1.3 78.2 - - + +
105A ASN* 1.3 69.8 + - - +
106A ILE* 3.4 28.4 + - + +
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Residues in contact with ASN 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 ALA 3.1 2.6 + - - -
102A ASN* 3.2 10.7 + - - +
103A LYS 3.1 7.7 - - - +
104A LEU* 1.3 82.1 - - - +
106A ILE* 1.3 61.1 + - - +
107A PRO* 3.5 10.4 - - - +
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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