Contacts of the helix formed by residues 85 - 94 (chain A) in PDB entry 3HS5
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 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LYS 3.9 1.8 + - - +
84A PRO* 1.3 76.9 - - - +
86A PRO* 1.3 74.6 - - + +
87A ASN* 3.6 8.9 + - - +
88A THR* 2.9 32.2 + - - +
89A VAL* 3.1 21.2 + - - +
520A GLU* 5.9 0.2 - - - -
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Residues in contact with PRO 86 (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 PRO 4.4 1.1 - - - +
85A THR* 1.3 87.4 - - + +
87A ASN* 1.3 55.6 + - - +
89A VAL* 3.3 6.6 + - + +
90A HIS* 2.9 30.8 + - - +
471A SER 5.0 7.0 - - - +
472A LEU* 3.7 26.0 - - + -
513A ARG* 3.9 9.3 + - - +
520A GLU* 4.0 10.3 - - - +
524A GLU* 3.6 34.4 - - + +
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Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A THR* 3.2 8.3 + - - +
86A PRO* 1.3 77.9 - - - +
88A THR* 1.3 56.1 - - - +
90A HIS* 3.7 5.4 + - - +
91A TYR* 3.1 26.7 + - - +
513A ARG* 2.9 35.8 + - - +
520A GLU* 3.9 21.5 + - - +
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PRO* 4.2 13.9 - - + -
85A THR* 2.9 31.8 + - - +
87A ASN* 1.3 75.6 - - - +
89A VAL* 1.3 64.6 + - - +
91A TYR* 3.2 8.7 + - + +
92A ILE* 3.0 38.2 + - + +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PRO* 3.8 27.6 - - + +
85A THR 3.1 14.8 + - - +
86A PRO* 3.7 8.7 - - + +
88A THR* 1.3 75.8 - - - +
90A HIS* 1.3 63.9 + - - +
92A ILE* 3.2 13.7 + - + +
93A LEU* 2.9 41.7 + - + +
115A TYR* 4.2 26.7 - - + +
120A ARG* 6.2 1.8 - - - +
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Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO 2.9 18.0 + - - +
87A ASN* 3.8 6.3 - - - +
89A VAL* 1.3 77.0 - - - +
91A TYR* 1.3 56.8 + - - +
93A LEU* 3.3 8.0 + - - -
94A THR* 2.8 61.4 + - + +
353A SER 4.0 7.0 - - - -
355A TYR* 4.2 12.1 + - + +
513A ARG* 3.6 44.7 + - + +
514A PRO* 4.9 9.1 + - + +
523A VAL* 6.1 0.8 - - - +
620A EDO 3.6 28.8 - - - -
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Residues in contact with TYR 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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87A ASN 3.1 16.0 + - - +
88A THR* 3.2 11.9 + - + +
90A HIS* 1.3 79.0 - - - +
92A ILE* 1.3 70.4 + - + +
94A THR* 3.2 5.4 + - - -
95A HIS* 2.7 76.4 + + - +
96A PHE* 4.0 23.9 - + - -
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Residues in contact with ILE 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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84A PRO* 6.0 2.2 - - + -
88A THR* 3.0 31.1 + - + +
89A VAL* 3.2 12.8 + - + +
91A TYR* 1.3 78.4 - - + +
93A LEU* 1.3 59.8 + - + +
95A HIS 3.1 13.5 + - - +
96A PHE* 3.7 24.1 - - + -
100A TRP* 3.0 36.1 + - + -
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Residues in contact with LEU 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 VAL* 2.9 39.7 + - + +
90A HIS* 3.8 3.1 - - - +
92A ILE* 1.3 77.1 - - + +
94A THR* 1.3 58.8 + - - +
95A HIS 3.5 0.4 - - - -
100A TRP* 3.7 31.9 + - + +
112A ILE* 5.2 5.2 - - + -
115A TYR* 6.1 2.2 - - + -
116A VAL* 5.7 8.1 - - + -
355A TYR* 3.4 49.1 - - + +
356A HIS* 3.0 30.3 + - - +
357A PHE* 4.0 22.0 + - + -
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Residues in contact with THR 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 HIS* 2.8 53.4 + - + +
91A TYR* 3.3 7.8 + - - -
92A ILE 3.2 0.4 - - - -
93A LEU* 1.3 79.4 - - - +
95A HIS* 1.3 78.9 + - - +
353A SER 4.4 0.2 - - - +
354A GLY* 3.5 27.8 - - - +
355A TYR* 4.2 3.6 - - + -
356A HIS* 3.5 18.7 + - - -
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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