Contacts of the helix formed by residues 89 - 97 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G GLN* 3.7 32.1 + - + +
51G LEU* 4.3 3.5 - - - +
87H SER* 2.9 10.1 + - - -
88H LYS* 1.3 82.1 - - - +
90H VAL* 1.3 66.0 + - - +
91H LYS* 3.7 9.6 + - - +
92H SER* 2.7 50.7 + - - +
93H THR* 3.4 5.9 + - - -
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Residues in contact with VAL 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H VAL* 4.3 20.0 - - + +
87H SER* 3.6 13.0 + - - -
89H ASP* 1.3 72.4 - - - +
91H LYS* 1.3 68.0 + - + +
93H THR* 2.9 4.8 + - - -
94H TYR* 2.9 58.2 + - + +
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Residues in contact with LYS 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004E SO4 3.9 33.6 + - - +
51G LEU* 4.0 20.0 - - + +
54G ARG* 4.4 11.1 - - - +
89H ASP* 3.3 9.2 + - - +
90H VAL* 1.3 84.8 - - + +
92H SER* 1.3 62.2 + - - +
94H TYR* 3.3 13.9 + - + +
95H THR* 2.9 32.3 + - - +
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Residues in contact with SER 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ASP* 3.7 10.0 - - - +
48G GLN* 3.2 39.1 - - - +
51G LEU* 3.3 19.4 - - - +
89H ASP* 2.7 30.8 + - - -
90H VAL 3.3 0.2 - - - -
91H LYS* 1.3 75.1 - - - +
93H THR* 1.3 54.0 + - - +
95H THR* 3.8 3.4 - - - -
96H THR* 2.7 38.0 + - - -
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Residues in contact with THR 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ASP* 4.7 9.4 + - - +
80H ILE* 6.0 1.6 - - + -
83H LEU* 4.4 7.2 + - + +
84H VAL* 4.0 33.9 - - + +
87H SER* 2.7 28.8 + - - -
89H ASP 3.4 0.9 + - - -
90H VAL* 2.9 10.1 + - - -
92H SER* 1.3 77.2 - - - +
94H TYR* 1.3 65.9 + - - +
96H THR* 3.1 13.2 + - - -
97H TYR* 3.2 39.4 + - + +
101H LEU* 5.3 0.4 - - + -
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Residues in contact with TYR 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H VAL* 4.2 23.6 - - + +
90H VAL* 2.9 43.6 + - + +
91H LYS* 3.7 14.1 - - + +
93H THR* 1.3 77.0 - - - +
95H THR* 1.3 62.0 + - - +
97H TYR 3.1 11.6 + - - -
98H ARG* 3.2 19.3 + - - +
101H LEU* 3.6 29.4 - - + +
119H LEU* 5.6 0.9 - - + -
120H GLU* 4.1 15.1 + - - +
121H ILE* 5.8 0.4 - - - -
122H ASN* 3.1 46.5 + - + +
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Residues in contact with THR 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004E SO4 4.2 3.1 + - - -
51G LEU* 4.6 10.9 - - + +
54G ARG* 4.2 15.5 + - - +
50H ASN* 5.4 0.3 - - - +
91H LYS* 2.9 28.5 + - - +
92H SER* 3.8 6.5 - - - -
94H TYR* 1.3 77.4 - - - +
96H THR* 1.3 62.0 + - - +
97H TYR 3.5 0.3 + - - -
98H ARG* 3.3 54.4 + - - +
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Residues in contact with THR 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ASP* 3.5 31.6 + - - +
50G ASN* 5.6 2.4 + - - +
96G THR* 3.8 34.6 + - + +
47H ASP* 4.8 0.7 - - - +
50H ASN* 3.3 15.1 - - - +
92H SER 2.7 22.8 + - - -
93H THR 3.1 5.6 + - - -
95H THR* 1.3 77.2 - - - +
97H TYR* 1.3 84.5 + - + +
98H ARG 3.6 0.2 - - - -
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Residues in contact with TYR 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ASP* 4.6 8.9 + - - -
46H LEU* 4.1 21.4 - - + +
47H ASP* 3.9 21.0 + - - -
50H ASN* 3.2 13.7 - - + +
80H ILE* 4.2 17.0 - - + -
83H LEU* 4.1 25.1 - - + +
93H THR* 3.2 37.6 + - + +
94H TYR 3.1 7.2 + - - +
96H THR* 1.3 100.4 - - + +
98H ARG* 1.3 57.8 + - - +
99H HIS 3.3 0.2 + - - -
100H ILE* 3.3 25.4 + - + -
101H LEU* 2.9 33.8 + - + +
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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