Contacts of the helix formed by residues 89 - 98 (chain A) in PDB entry 5HVM
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLU* 3.6 18.8 - - - +
87A PHE 4.9 0.9 - - - +
88A ILE* 1.3 76.0 - - - +
90A ASP* 1.3 61.0 + - - +
91A GLU* 3.3 26.1 - - - +
92A LEU* 3.3 22.2 + - - +
93A ALA* 2.9 26.9 + - - +
132A LEU* 5.3 4.5 - - - +
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Residues in contact with ASP 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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60A TRP* 4.9 6.1 - - - -
62A GLY 4.7 2.8 - - - +
63A LEU* 4.1 8.7 - - - +
64A GLU* 3.5 45.3 + - + +
88A ILE 5.1 0.3 - - - +
89A ASP* 1.3 73.4 - - - +
91A GLU* 1.3 70.8 + - - +
93A ALA* 3.9 4.4 - - - +
94A ASP* 3.1 25.6 + - - +
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Residues in contact with GLU 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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64A GLU* 4.2 7.6 - - - +
89A ASP* 3.3 29.8 - - - +
90A ASP* 1.3 85.8 + - - +
92A LEU* 1.3 62.6 + - + +
94A ASP* 3.7 5.6 - - - +
95A ARG* 3.5 30.3 + - - +
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Residues in contact with LEU 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 ILE* 3.5 21.8 - - + -
89A ASP* 3.3 24.7 + - - +
91A GLU* 1.3 77.3 - - + +
93A ALA* 1.3 67.3 + - - +
94A ASP 3.1 1.3 - - - -
95A ARG* 3.1 25.6 + - - +
96A HIS* 3.0 19.9 + - - +
125A ALA* 4.0 11.6 - - + +
128A GLU* 3.4 39.7 - - + +
129A ALA* 4.0 25.8 - - + +
132A LEU* 5.2 4.9 - - + -
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Residues in contact with ALA 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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60A TRP* 3.7 36.8 - - + +
88A ILE* 3.5 19.1 - - + +
89A ASP 2.9 18.2 + - - +
90A ASP* 3.9 5.4 - - - +
92A LEU* 1.3 76.3 - - - +
94A ASP* 1.3 52.3 + - - +
96A HIS* 3.4 6.6 + - - +
97A TYR* 2.7 40.4 + - - +
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Residues in contact with ASP 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 ASP 3.1 19.1 + - - +
91A GLU* 3.7 7.8 - - - +
92A LEU 3.1 0.2 - - - -
93A ALA* 1.3 74.2 - - - +
95A ARG* 1.3 65.4 + - - +
97A TYR* 4.5 1.6 - - - +
98A ASN* 2.8 58.0 + - - +
99A GLY 3.0 5.5 + - - -
327A ASP* 5.1 2.8 - - - +
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Residues in contact with ARG 95 (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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91A GLU* 3.5 16.9 + - - +
92A LEU* 3.1 33.4 + - - +
94A ASP* 1.3 82.9 - - - +
96A HIS* 1.3 57.8 + - - +
99A GLY* 2.9 28.3 - - - +
100A PHE* 3.0 8.0 + - - +
121A SER* 3.4 36.9 + - - +
122A ALA* 4.2 7.7 - - + +
124A GLU* 4.7 8.7 + - - +
125A ALA* 3.4 29.6 - - + +
128A GLU* 5.6 2.8 + - - -
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Residues in contact with HIS 96 (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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19A ASN* 3.4 25.0 + - - -
60A TRP* 6.5 0.7 - + - -
88A ILE* 4.9 9.4 - - + -
92A LEU 3.0 15.6 + - - +
93A ALA* 3.7 7.2 - - + +
95A ARG* 1.3 76.4 - - - +
97A TYR* 1.3 69.0 + - + +
100A PHE* 3.5 4.6 + - - +
101A SER* 3.0 33.0 + - - -
125A ALA* 3.6 20.6 - - - +
126A TYR* 3.5 27.6 - + - +
129A ALA* 3.4 21.2 - - + +
130A ASN* 3.9 9.6 - - - -
133A PHE* 5.2 1.8 - - - -
153A HIS* 3.4 25.5 + - + +
154A LEU* 5.0 3.8 - - + +
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Residues in contact with TYR 97 (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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19A ASN* 3.4 28.9 - - - +
20A ARG* 3.1 31.0 + - - -
60A TRP* 4.7 14.6 - + + -
93A ALA* 2.7 22.8 + - - +
94A ASP* 4.8 0.7 - - - -
96A HIS* 1.3 82.9 - - + +
98A ASN* 1.3 81.5 + - - +
101A SER* 3.4 6.5 - - - -
102A ASN* 2.9 48.5 + - - -
153A HIS* 3.8 21.5 - + - -
325A ARG* 4.6 14.1 + - + +
602A VDM 4.4 12.5 + - - -
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Residues in contact with ASN 98 (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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94A ASP* 2.8 37.3 + - - +
97A TYR* 1.3 86.3 - - - +
99A GLY* 1.3 59.2 + - - +
102A ASN* 3.1 24.2 + - - +
103A SER* 2.4 35.3 + - - -
325A ARG* 5.2 2.6 - - - +
327A ASP* 3.8 28.8 + - + +
328A VAL* 4.1 16.3 - - + +
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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