Contacts of the helix formed by residues 88 - 97 (chain A) in PDB entry 5HOO
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A GLN* 1.3 73.9 - - - +
89A GLN* 1.3 62.5 + - - +
90A LYS* 4.1 11.0 + - + +
91A GLN* 2.9 62.3 + - + +
92A LEU* 3.2 11.8 + - - +
7C G 3.3 43.4 + - - +
8C T 3.4 13.5 + - - -
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Residues in contact with GLN 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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87A GLN 3.8 0.6 + - - -
88A THR* 1.3 71.8 + - - +
90A LYS* 1.3 56.2 + - - +
92A LEU* 3.5 8.4 + - + +
93A ALA* 2.9 31.1 + - - +
100A GLN* 2.6 43.2 + - + +
103A VAL* 3.5 16.4 - - + +
104A SER* 3.4 20.5 - - - +
107A LEU* 4.1 10.1 - - + +
171B TYR* 3.1 33.2 + - + -
8C T 3.0 29.6 + - - +
9C A 3.1 23.6 + - - -
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Residues in contact with LYS 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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88A THR* 3.2 11.9 + - + +
89A GLN* 1.3 78.5 - - - +
91A GLN* 1.3 60.6 + - - +
93A ALA* 3.7 6.8 - - + +
94A GLU* 3.2 41.9 + - + +
100A GLN* 4.3 16.6 - - + +
7C G 4.4 15.3 + - - +
8C T 4.7 1.0 + - + -
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Residues in contact with GLN 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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84A ASP* 5.3 1.4 + - - -
86A ALA 5.2 0.6 + - - -
87A GLN* 3.2 32.2 - - + +
88A THR* 2.9 36.0 + - + +
90A LYS* 1.3 77.0 - - - +
92A LEU* 1.3 64.5 + - - +
94A GLU* 3.5 14.3 + - - +
95A GLN* 3.4 27.2 + - - +
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Residues in contact with LEU 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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77A LEU* 4.1 23.6 - - + -
80A LEU* 4.2 16.3 - - + +
81A LEU* 4.2 21.8 - - + -
87A GLN* 3.7 38.6 - - + +
88A THR 3.2 16.3 + - - +
89A GLN* 3.8 16.4 - - + +
91A GLN* 1.3 72.0 - - - +
93A ALA* 1.3 67.2 + - - +
95A GLN* 3.1 12.5 + - - +
96A LEU* 3.0 28.8 + - + +
103A VAL* 4.5 11.2 - - + -
107A LEU* 4.9 12.3 - - + -
171B TYR* 5.0 2.0 - - + -
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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 GLN 2.9 19.1 + - - +
90A LYS* 3.7 7.4 - - + +
92A LEU* 1.3 76.2 - - - +
94A GLU* 1.3 56.5 + - + +
96A LEU 3.5 0.5 + - - -
97A GLU* 2.9 24.8 + - - -
98A VAL* 3.0 31.8 + - - +
99A SER 3.4 22.7 - - - +
100A GLN* 3.7 4.3 - - - +
103A VAL* 4.3 10.9 - - + +
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Residues in contact with GLU 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 LYS* 3.2 37.6 + - + +
91A GLN* 3.7 14.8 - - - +
92A LEU 3.3 0.4 - - - -
93A ALA* 1.3 77.8 - - + +
95A GLN* 1.3 62.8 + - + +
97A GLU* 3.4 15.6 + - - +
98A VAL 5.0 0.4 - - - -
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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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80A LEU* 3.6 32.9 - - + +
83A GLU* 5.0 4.2 + - - -
87A GLN* 2.6 32.8 + - - +
91A GLN* 3.4 13.4 + - - +
92A LEU* 3.1 6.4 + - - +
94A GLU* 1.3 79.1 - - + +
96A LEU* 1.3 60.6 + - - +
97A GLU* 3.4 9.0 + - - +
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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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71A ARG* 5.4 3.5 - - - +
72A TYR* 3.9 51.4 - - + +
76A GLU* 4.1 33.5 - - + +
77A LEU* 4.1 16.2 - - + +
80A LEU* 4.6 10.1 - - + -
92A LEU 3.0 17.0 + - - +
93A ALA 4.1 0.2 - - - +
95A GLN* 1.3 72.7 - - - +
97A GLU* 1.3 69.7 + - - +
98A VAL* 3.4 18.9 + - + +
103A VAL* 3.7 29.6 - - + -
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Residues in contact with GLU 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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71A ARG* 5.2 3.5 + - - +
93A ALA 2.9 7.5 + - - -
94A GLU* 3.4 10.2 + - - +
95A GLN 3.2 11.8 - - - +
96A LEU* 1.3 81.9 - - - +
98A VAL* 1.3 62.5 + - - +
45D T 4.2 4.3 + - - -
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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