Contacts of the helix formed by residues 85 - 93 (chain A) in PDB entry 1HPL
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 TRP 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ILE* 3.6 26.9 - - + -
74A ILE 4.5 2.9 - - - -
75A HIS* 4.0 17.7 - - - +
77A PHE 4.7 8.2 + - - -
78A ILE* 4.8 6.8 - - + +
82A GLU* 3.1 29.8 + - + +
83A GLU 3.4 1.0 - - - -
84A SER* 1.3 75.0 - - - +
86A LEU* 1.3 86.8 + - + +
88A THR* 3.4 7.4 + - - -
89A MET* 3.1 47.1 + - + +
149A ILE* 5.5 0.7 - - + -
151A HIS* 3.8 32.3 - - + -
175A LEU* 4.9 3.8 - - + -
267A TYR* 3.5 59.5 - + + +
271A THR* 5.2 2.2 + - - -
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Residues in contact with LEU 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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73A ILE* 3.7 38.3 - - + +
75A HIS* 4.0 29.2 - - + +
78A ILE* 4.7 7.6 - - + -
83A GLU 4.6 11.0 - - - +
84A SER 3.2 1.2 - - - -
85A TRP* 1.3 119.3 - - + +
87A SER* 1.3 63.4 + - - +
89A MET* 3.2 6.0 + - - +
90A CYS* 3.1 18.9 + - - -
103A CYS* 3.7 25.1 - - + -
104A VAL 4.5 6.5 - - - +
107A LYS* 5.6 2.2 - - - +
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 3.6 33.8 + - - -
84A SER* 3.3 20.3 + - - -
86A LEU* 1.3 78.3 - - - +
88A THR* 1.4 59.7 + - - +
90A CYS* 3.4 5.6 + - - +
91A GLN* 2.9 41.7 + - - +
103A CYS* 4.2 6.7 - - - -
441B ASP* 5.3 3.3 + - - -
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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
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84A SER* 2.9 38.6 + - - +
85A TRP* 4.2 6.0 + - - -
87A SER* 1.4 76.2 - - - +
89A MET* 1.4 65.1 + - - +
91A GLN* 3.2 15.2 + - - +
92A ASN* 3.1 27.8 + - - +
271A THR* 4.3 12.6 - - - +
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Residues in contact with MET 89 (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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73A ILE* 3.9 17.3 - - + -
85A TRP* 3.1 39.3 + - + +
86A LEU* 3.4 10.1 - - - +
88A THR* 1.4 78.2 + - - +
90A CYS* 1.3 61.5 + - - +
92A ASN 3.4 5.9 + - - -
93A MET* 3.5 27.3 + - + +
149A ILE* 4.3 11.7 - - - -
175A LEU* 4.4 3.1 - - + -
267A TYR* 3.8 14.1 - - + +
270A TYR* 3.7 32.3 - - + -
271A THR* 3.6 27.5 - - - +
274A ILE* 3.7 14.8 - - + +
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Residues in contact with CYS 90 (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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41A TYR* 4.3 9.4 - - + -
73A ILE* 3.8 2.9 - - - -
86A LEU 3.1 8.4 + - - -
87A SER* 3.4 8.5 + - - +
89A MET* 1.3 74.7 - - - +
91A GLN* 1.3 60.8 + - - +
93A MET* 3.1 17.3 + - - +
94A PHE* 3.3 25.9 + - + -
101A CYS* 2.0 57.9 - - + -
103A CYS* 3.7 28.9 - - - -
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Residues in contact with GLN 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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41A TYR* 4.3 2.6 - - - -
46A PRO* 2.7 33.0 + - + +
47A ASP* 3.9 18.1 + - - +
87A SER* 2.9 33.8 + - - +
88A THR* 3.2 18.1 + - - +
90A CYS* 1.3 74.0 - - + +
92A ASN* 1.3 64.6 + - - +
94A PHE* 3.7 20.1 + - + +
95A LYS* 3.8 18.6 + - - +
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Residues in contact with ASN 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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88A THR* 3.1 11.9 + - - +
89A MET 3.8 8.5 - - - +
90A CYS 3.3 0.2 - - - -
91A GLN* 1.3 75.9 - - - +
93A MET* 1.3 65.6 + - - +
95A LYS* 3.0 41.0 + - - +
96A VAL 3.8 1.0 + - - -
271A THR* 3.1 36.9 + - - +
272A ASP* 5.1 2.4 + - - +
274A ILE* 3.7 23.6 - - + +
275A LEU* 3.5 25.7 - - + +
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Residues in contact with MET 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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71A ARG* 3.7 32.8 - - + -
73A ILE* 4.1 10.5 - - + -
89A MET* 3.5 35.4 - - + +
90A CYS 3.1 6.4 + - - +
92A ASN* 1.3 73.8 - - - +
94A PHE* 1.4 57.6 + - - +
96A VAL* 2.9 24.2 + - - +
97A GLU* 3.1 30.4 + - - +
99A VAL* 4.0 12.1 - - + -
101A CYS* 4.0 18.2 - - - -
149A ILE* 4.1 16.6 - - + -
270A TYR* 4.6 3.8 - - + -
274A ILE* 3.9 18.8 - - + +
309A HIS* 4.2 5.8 - - + -
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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