Contacts of the helix formed by residues 93 - 101 (chain A) in PDB entry 5F85
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 THR 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A THR* 5.6 8.7 - - + +
91A GLY 4.9 2.5 - - - +
92A VAL* 1.3 77.2 - - - +
94A ARG* 1.3 57.2 + - - +
95A GLN* 3.1 13.4 + - - +
96A MET* 2.8 59.7 + - + +
97A ILE* 3.2 9.9 + - - +
392A GLN* 4.7 11.9 - - + -
393A TYR* 3.9 2.0 - - - -
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Residues in contact with ARG 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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93A THR* 1.3 72.2 - - - +
95A GLN* 1.3 55.7 + - - +
97A ILE* 3.3 5.7 + - + +
98A GLU* 2.9 52.2 + - + +
392A GLN 4.9 0.2 + - - -
393A TYR* 3.4 42.7 - - + +
394A GLU* 2.6 45.3 + - - +
396A LYS* 3.2 33.1 - - - +
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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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93A THR* 3.0 10.9 + - - +
94A ARG* 1.3 79.5 - - - +
96A MET* 1.3 52.5 + - + +
98A GLU* 3.4 19.2 + - - +
99A SER* 2.7 50.3 + - - +
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Residues in contact with MET 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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87A TYR* 3.9 30.3 - - + -
90A THR* 5.9 4.3 - - - -
91A GLY 3.6 18.8 - - - +
92A VAL* 3.9 7.6 - - + -
93A THR* 2.8 52.9 + - + +
95A GLN* 1.3 71.9 - - + +
97A ILE* 1.3 53.4 + - - +
99A SER* 3.3 6.8 + - - -
100A SER* 2.8 38.2 + - - -
164A GLY* 4.6 6.1 - - - +
165A GLY 3.5 15.4 - - - +
166A PRO* 4.7 0.4 - - + -
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Residues in contact with ILE 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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92A VAL* 3.7 24.0 - - + -
93A THR 3.2 3.0 + - - +
94A ARG* 3.5 10.1 - - + +
96A MET* 1.3 76.0 - - - +
98A GLU* 1.3 60.3 + - + +
100A SER* 3.3 4.7 + - - -
101A ALA* 3.0 27.2 + - - +
106A LYS* 4.1 16.6 - - - +
144A ASP* 3.7 30.3 - - + +
146A ILE* 4.1 16.3 - - + +
166A PRO* 4.1 10.1 - - + +
387A TYR* 3.5 24.7 - - - +
391A LEU* 5.7 0.4 - - + -
393A TYR* 3.4 23.3 - - + +
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Residues in contact with GLU 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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94A ARG* 2.9 41.8 + - + +
95A GLN* 3.6 24.3 - - - +
97A ILE* 1.3 76.4 - - + +
99A SER* 1.3 64.0 + - - +
100A SER 3.5 0.3 + - - -
101A ALA* 3.6 17.1 + - - +
102A ARG* 4.9 6.2 + - - -
106A LYS* 5.7 6.3 - - - +
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Residues in contact with SER 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 GLN* 2.7 34.8 + - - +
96A MET* 3.4 10.1 - - - -
98A GLU* 1.3 75.9 - - - +
100A SER* 1.3 60.5 + - - +
101A ALA 3.7 0.2 + - - -
102A ARG* 3.6 28.2 + - - +
103A TYR* 4.3 5.4 - - - -
161A ASN 5.7 0.5 + - - -
162A ALA* 4.8 11.6 + - - +
165A GLY 5.6 0.2 - - - -
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Residues in contact with SER 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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96A MET 2.8 17.4 + - - -
97A ILE* 3.3 4.5 + - - -
99A SER* 1.3 75.0 - - - +
101A ALA* 1.3 67.0 + - - +
102A ARG 3.0 3.1 - - - -
103A TYR* 2.8 28.5 + - - +
146A ILE* 3.3 13.7 - - - +
165A GLY* 2.9 26.2 + - - -
166A PRO 3.9 8.7 - - - -
167A VAL* 3.7 20.6 - - - -
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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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97A ILE 3.0 14.3 + - - +
98A GLU* 3.9 11.4 - - - +
99A SER 3.5 2.0 - - - -
100A SER* 1.3 76.5 - - - +
102A ARG* 1.3 56.6 + - - +
103A TYR 3.2 0.2 + - - -
104A GLY 3.1 24.5 + - - +
106A LYS* 4.5 20.5 + - + +
117A ASP* 5.4 1.4 - - - +
146A ILE* 3.8 19.9 - - + +
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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