Contacts of the helix formed by residues 65 - 70 (chain H) in PDB entry 1HWT
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 65 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLU* 5.8 6.7 - - + -
63H SER 3.8 1.0 + - - -
64H CYS* 1.3 71.7 - - - +
66H ILE* 1.3 65.5 + - - +
68H ARG* 3.4 26.8 + - - +
69H LYS* 2.9 45.1 + - - +
92H LEU 4.6 0.2 + - - -
94H HIS* 3.2 49.5 + - + +
95H TYR* 5.0 0.2 - - - +
96H MET* 4.4 21.8 - - + +
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Residues in contact with ILE 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D LEU* 3.7 33.0 - - + -
64H CYS* 3.1 1.4 - - - -
65H THR* 1.3 77.7 + - - +
67H CYS* 1.3 58.5 - - - +
69H LYS* 3.1 6.8 + - - +
70H ARG* 2.7 68.2 + - - +
72H VAL* 6.2 0.4 - - + -
84H CYS* 3.7 27.4 - - - -
87H THR* 6.0 0.2 - - - +
89H VAL* 4.5 7.4 - - + -
92H LEU* 3.8 39.7 - - + +
93H CYS* 4.6 2.2 - - - -
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Residues in contact with CYS 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H SER* 4.8 1.8 - - - -
64H CYS* 3.2 6.9 + - - +
66H ILE* 1.3 78.2 - - - +
68H ARG* 1.3 53.8 + - - +
71H LYS* 2.5 30.3 + - - -
72H VAL* 2.9 29.0 + - + +
74H CYS* 3.6 22.7 - - + -
81H CYS* 3.9 0.7 - - - -
83H GLN* 3.5 32.3 - - - -
84H CYS* 4.9 2.0 - - - -
136H ZN 2.3 36.1 - - - -
137H ZN 4.4 0.2 - - - -
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Residues in contact with ARG 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLU* 6.2 1.6 - - - +
15F T 5.4 1.8 - - - -
16F A 3.2 28.3 - - + +
61H PRO* 3.6 24.0 - - + +
63H SER* 4.9 8.6 + - - +
64H CYS 3.1 15.3 + - - +
65H THR* 3.6 27.4 + - - +
67H CYS* 1.3 78.3 - - - +
69H LYS* 1.3 77.9 + - - +
71H LYS* 3.3 19.3 + - - +
96H MET* 3.6 26.4 - - - +
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Residues in contact with LYS 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLU* 3.3 39.4 + - - +
102D GLU* 3.8 12.4 + - - +
105D GLU* 3.4 28.1 - - - +
106D LYS* 5.8 2.0 - - - +
109D LEU* 4.2 23.1 - - + +
1E G 5.4 4.0 - - - +
2E C 4.9 10.9 + - - -
65H THR* 2.9 32.3 + - - +
66H ILE* 3.7 4.3 - - + +
68H ARG* 1.3 93.6 - - - +
70H ARG* 1.3 61.8 + - - +
71H LYS* 3.6 4.2 + - - +
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Residues in contact with ARG 70 (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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118C ARG* 3.2 21.5 + - - +
109D LEU* 2.6 52.7 + - - +
112D ASN* 3.1 20.8 + - - -
113D GLU* 3.1 48.9 - - - +
116D LYS* 5.8 1.0 - - - +
1E G 6.0 2.0 - - - -
2E C 3.4 5.7 + - - -
66H ILE* 2.7 40.1 + - - +
67H CYS 4.0 1.6 - - - +
69H LYS* 1.3 73.9 - - - +
71H LYS* 1.3 70.7 + - - +
72H VAL* 3.8 16.5 - - + +
87H THR* 4.1 13.9 + - - -
89H VAL* 4.1 17.0 - - - +
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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