Contacts of the helix formed by residues 87 - 94 (chain A) in PDB entry 1H4L
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 LEU 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLN 4.1 0.2 + - - -
86A ASP* 1.3 72.5 - - - +
88A LYS* 1.3 57.0 + - - +
90A TYR* 3.2 11.5 - - + +
91A PHE* 2.9 53.0 + - + -
106A PHE* 4.0 14.4 - - + -
129A PRO* 3.3 21.0 + - + +
132A LEU* 2.7 41.2 + - + +
134A ILE* 3.2 28.6 - - + +
140A LEU* 5.1 4.0 - - + -
191A ILE* 4.6 7.6 - - + -
195A LEU* 4.0 17.7 - - + -
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Residues in contact with LYS 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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86A ASP* 2.7 21.3 + - - +
87A LEU* 1.3 74.4 - - - +
89A LYS* 1.3 58.9 + - - +
91A PHE* 3.2 24.5 + - + +
92A ASP* 3.4 10.5 + - - +
129A PRO* 3.6 13.0 + - + -
130A GLN* 3.7 46.1 + - + +
166A TRP* 4.6 11.3 - - - -
167A TYR* 4.7 3.4 + - - -
194A GLU* 4.6 7.1 + - - +
201A PRO* 4.6 6.9 - - - +
92B ASP* 3.0 30.7 + - - -
200B ARG* 4.7 0.5 + - - -
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Residues in contact with LYS 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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84A ASP 5.7 1.2 + - - -
85A GLN* 3.5 25.2 - - + +
86A ASP* 2.6 28.6 + - - +
88A LYS* 1.3 70.0 - - - +
90A TYR* 1.3 65.9 + - - +
92A ASP* 2.8 11.6 + - - +
93A SER* 2.8 21.1 + - - -
166B TRP* 3.9 33.9 - - + +
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Residues in contact with TYR 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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85A GLN* 3.6 21.6 + - + -
86A ASP 3.0 9.8 + - - +
87A LEU* 3.2 32.1 - - + +
89A LYS* 1.3 76.4 - - - +
91A PHE* 1.3 64.1 + + - +
93A SER* 2.8 34.3 + - - -
94A CYS* 3.3 28.3 + - + +
98A LEU* 4.0 11.2 - - + -
102A ILE* 3.5 29.1 - - - +
106A PHE* 3.9 24.6 - + - -
134A ILE* 4.2 20.0 - - + -
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Residues in contact with PHE 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 LEU* 2.9 35.5 + - + -
88A LYS* 3.2 18.4 + - + +
90A TYR* 1.3 78.7 - + - +
92A ASP* 1.3 57.3 + - - +
94A CYS* 2.8 19.0 - - - +
95A ASN* 3.9 2.4 - - - -
96A GLY 4.8 0.7 + - - -
98A LEU* 3.8 22.0 - - + -
129A PRO* 4.5 3.8 - - + -
194A GLU* 3.7 23.1 - - + -
195A LEU* 3.5 46.4 - - + -
199A ALA* 3.2 42.2 - - + +
200B ARG* 3.3 26.7 + - - +
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Residues in contact with ASP 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 LYS* 3.4 7.9 + - - +
89A LYS* 2.8 13.9 + - - +
91A PHE* 1.3 73.9 - - - +
93A SER* 1.3 64.9 + - - +
94A CYS 2.6 14.6 - - - +
95A ASN* 4.7 1.7 - - - +
200A ARG* 4.8 0.9 + - - -
88B LYS* 2.8 35.1 + - - -
166B TRP* 3.6 20.8 - - + -
199B ALA 4.7 2.1 - - - +
200B ARG* 2.6 36.3 + - - +
201B PRO* 3.5 20.7 - - + +
204B PRO* 3.9 9.5 - - - +
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Residues in contact with SER 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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85A GLN* 2.9 34.6 + - - -
89A LYS* 2.8 10.2 + - - +
90A TYR* 2.8 14.8 + - - -
92A ASP* 1.3 78.2 - - - +
94A CYS* 1.3 63.6 + - - +
95A ASN* 5.1 0.7 - - - +
166B TRP* 4.5 5.1 - - - -
204B PRO* 3.1 33.7 - - - +
206B ASN* 6.0 3.8 - - - -
214B ARG* 4.4 7.0 + - - -
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Residues in contact with CYS 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 TYR* 3.7 37.7 - - + -
91A PHE* 2.8 13.6 - - - +
92A ASP 2.6 19.8 - - - +
93A SER* 1.3 80.2 - - - +
95A ASN* 1.3 65.2 + - - +
97A ASP 3.8 19.3 - - - +
98A LEU* 4.3 11.2 - - - -
214B ARG* 5.9 0.7 - - - +
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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