Contacts of the helix formed by residues 89 - 97 (chain F) in PDB entry 2HQT
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 ASP 89 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ALA* 6.3 1.6 - - - +
48E GLN* 3.6 32.8 + - + +
51E LEU* 4.5 5.9 - - - +
52E VAL* 6.0 0.3 - - - +
87F SER* 2.9 12.0 + - - -
88F LYS* 1.3 82.7 - - - +
90F VAL* 1.3 63.4 + - - +
91F LYS* 3.0 13.3 + - - +
92F SER* 2.9 45.2 + - - +
93F THR* 3.3 6.8 + - - -
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Residues in contact with VAL 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA* 4.2 26.7 - - + +
84F VAL* 4.1 17.7 - - + +
87F SER* 3.7 20.9 - - - +
89F ASP* 1.3 72.8 + - - +
91F LYS* 1.3 63.3 + - - +
93F THR* 3.0 5.6 + - - -
94F TYR* 3.0 56.9 + - + +
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Residues in contact with LYS 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LEU* 3.7 21.7 - - + +
54E ARG* 4.2 10.7 - - - +
55E ASP* 5.4 1.2 + - - -
2003E SO4 3.7 35.0 + - - +
89F ASP* 3.0 8.4 + - - +
90F VAL* 1.3 76.3 - - - +
92F SER* 1.3 63.1 + - - +
94F TYR* 3.2 12.7 + - + +
95F THR* 3.0 31.8 + - + +
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Residues in contact with SER 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ASP* 3.5 28.3 + - - -
48E GLN* 3.3 15.4 - - - -
51E LEU* 3.4 12.9 - - - +
89F ASP* 2.9 37.7 + - - -
91F LYS* 1.3 75.0 - - - +
93F THR* 1.3 55.5 + - - +
95F THR* 2.8 17.5 + - - -
96F THR* 2.7 30.0 + - - -
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Residues in contact with THR 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ASP* 4.6 9.3 + - - +
80F ILE* 5.8 1.3 - - + -
83F LEU* 4.3 8.2 + - + +
84F VAL* 4.1 35.2 - - + +
87F SER* 2.7 29.9 + - - -
89F ASP 3.4 0.7 + - - -
90F VAL* 3.0 9.3 + - - -
92F SER* 1.3 77.4 - - - +
94F TYR* 1.3 65.0 + - - +
96F THR* 3.1 14.2 + - - -
97F TYR* 3.2 34.5 + - + +
101F LEU* 5.0 0.4 - - - +
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Residues in contact with TYR 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F VAL* 4.1 26.3 - - + +
90F VAL* 3.0 42.0 + - + +
91F LYS* 3.2 13.2 + - + +
93F THR* 1.3 78.4 - - + +
95F THR* 1.3 62.8 + - + +
97F TYR 3.4 1.2 + - - -
98F ARG* 3.2 32.4 + - - +
101F LEU* 3.6 26.8 - - + +
119F LEU* 5.1 7.6 - - + -
120F GLU 4.1 13.2 + - - -
121F ILE* 4.6 17.5 - - + -
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Residues in contact with THR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ASP 5.4 0.3 + - - -
51E LEU* 3.9 12.1 - - + +
54E ARG* 4.4 9.0 - - - +
2003E SO4 3.4 25.8 - - - +
50F ASN* 5.5 0.2 - - - +
91F LYS* 3.0 23.5 + - + +
92F SER* 2.8 24.4 + - - -
94F TYR* 1.3 76.6 - - + +
96F THR* 1.3 61.3 + - - +
97F TYR 3.4 0.2 - - - -
98F ARG* 3.5 36.0 + - - +
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Residues in contact with THR 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ASP* 3.3 40.9 + - - +
50E ASN* 5.4 4.5 + - - -
96E THR* 3.9 30.3 + - + +
47F ASP* 5.5 0.2 - - - +
50F ASN* 3.2 15.6 - - - +
92F SER 2.7 20.4 + - - -
93F THR 3.1 6.0 + - - -
95F THR* 1.3 80.6 + - - +
97F TYR* 1.3 80.6 + - + +
98F ARG 3.7 0.4 - - - -
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Residues in contact with TYR 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ASP* 4.4 9.7 + - - -
46F LEU* 4.1 19.4 - - + +
47F ASP* 3.8 22.7 + - - -
50F ASN* 3.2 13.7 - - + +
80F ILE* 4.0 16.4 - - + -
83F LEU* 3.8 31.3 - - + +
93F THR* 3.2 36.8 + - + +
94F TYR 3.6 3.4 - - - -
96F THR* 1.3 102.5 - - + +
98F ARG* 1.3 64.0 + - - +
99F HIS 3.2 0.2 + - - -
100F ILE* 3.4 27.6 + - + -
101F LEU* 2.8 29.6 + - + +
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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