Contacts of the helix formed by residues 89 - 97 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87G SER* 2.9 9.9 + - - -
88G LYS* 1.3 80.9 - - + +
90G VAL* 1.3 63.9 + - - +
91G LYS* 3.4 10.7 + - - +
92G SER* 2.7 46.5 + - - +
93G THR 3.2 2.3 + - - -
48H GLN* 3.1 44.4 - - + +
51H LEU* 4.9 5.8 - - - +
116I THR* 3.9 4.8 + - - -
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Residues in contact with VAL 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G VAL* 3.9 22.2 - - + +
87G SER* 3.2 10.2 + - - +
89G ASP* 1.3 73.8 + - - +
91G LYS* 1.3 62.0 + - + +
93G THR* 3.0 5.3 + - - -
94G TYR* 2.8 69.2 + - + +
116I THR* 3.7 31.1 + - + +
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Residues in contact with LYS 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2003E SO4 4.1 30.1 + - - +
89G ASP* 3.3 9.1 + - - +
90G VAL* 1.3 81.3 - - + +
92G SER* 1.3 63.7 + - - +
94G TYR* 3.3 13.1 + - + +
95G THR* 3.0 30.6 + - - +
51H LEU* 3.9 25.9 - - + +
54H ARG* 4.4 10.0 - - - +
55H ASP* 5.5 0.8 + - - -
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Residues in contact with SER 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G SER* 4.9 0.2 + - - -
89G ASP* 2.7 34.7 + - - +
91G LYS* 1.3 77.8 - - - +
93G THR* 1.3 61.8 + - - +
95G THR* 3.4 4.5 + - - -
96G THR* 2.7 30.4 + - - -
47H ASP* 3.6 31.0 - - - +
48H GLN* 3.6 16.1 + - - +
51H LEU* 3.9 15.8 - - - +
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Residues in contact with THR 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G LEU* 4.2 11.0 - - + +
84G VAL* 3.9 33.0 - - + -
87G SER* 2.6 31.4 + - - -
89G ASP 3.2 1.1 + - - -
90G VAL* 3.0 11.1 + - - -
92G SER* 1.3 79.8 + - - +
94G TYR* 1.3 63.8 + - - +
96G THR* 3.1 14.0 + - - -
97G TYR* 3.1 37.5 + - + +
101G LEU* 6.3 0.4 - - + -
47H ASP* 4.7 8.0 + - - +
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Residues in contact with TYR 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G VAL* 4.1 25.9 - - + +
90G VAL* 2.8 56.2 + - + +
91G LYS* 3.3 10.3 + - + +
93G THR* 1.3 73.7 - - - +
95G THR* 1.3 60.7 + - - +
97G TYR 3.4 1.4 + - - -
98G ARG* 3.2 31.6 + - - +
101G LEU* 3.7 27.0 - - + +
119G LEU* 5.9 0.9 - - + -
120G GLU* 3.8 29.2 + - - -
121G ILE* 6.4 0.2 - - - -
122G ASN* 5.0 22.0 - - + +
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Residues in contact with THR 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2003E SO4 4.3 2.8 + - - -
50G ASN* 5.4 0.3 - - - +
91G LYS* 3.0 26.5 + - - +
92G SER* 3.6 8.5 - - - -
94G TYR* 1.3 76.2 - - - +
96G THR* 1.3 63.9 + - - +
98G ARG* 3.4 50.8 + - - +
50H ASN* 6.0 2.9 - - - +
51H LEU* 4.4 14.9 - - + +
54H ARG* 4.3 14.4 - - - +
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Residues in contact with THR 96 (chain G).
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* 5.3 0.5 - - - +
50G ASN* 3.2 15.9 - - - +
92G SER 2.7 20.7 + - - -
93G THR 3.1 5.1 + - - -
95G THR* 1.3 80.3 - - - +
97G TYR* 1.4 83.8 + - + +
98G ARG 3.7 0.7 - - - -
47H ASP* 3.4 36.2 + - - +
50H ASN* 5.6 2.4 + - - +
96H THR* 3.8 31.3 + - + +
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Residues in contact with TYR 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G LEU* 4.4 17.2 - - + +
47G ASP* 3.8 22.1 + - - -
50G ASN* 3.3 12.1 - - + +
80G ILE* 4.2 16.6 - - + -
83G LEU* 4.0 30.7 - - + +
93G THR* 3.1 39.2 + - + +
94G TYR 3.5 3.8 - - - -
96G THR* 1.4 99.8 - - + +
98G ARG* 1.3 63.5 + - - +
99G HIS 3.2 3.1 + - - -
100G ILE* 3.4 25.0 + - + -
101G LEU* 2.9 30.2 + - + +
47H ASP* 4.6 8.2 + - - -
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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