Contacts of the helix formed by residues 87 - 100 (chain A) in PDB entry 3VPM
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 TYR 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A PRO* 3.6 25.2 + - + +
72A LEU* 4.9 5.4 - - + -
74A ARG* 5.2 3.3 + - - -
85A ILE* 4.1 2.2 - - - -
86A GLU* 1.3 86.1 - - + +
88A HIS* 1.3 60.3 + - - +
89A ASP* 3.3 6.3 - - - +
90A ILE* 3.3 32.4 + - + -
91A TRP* 2.9 27.9 + - - +
155A ILE* 3.6 26.8 - - + +
157A GLU* 2.8 28.6 + - + +
279A HIS* 4.0 23.3 - + - -
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Residues in contact with HIS 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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85A ILE* 3.7 36.8 + - + +
86A GLU* 3.5 11.9 + - - -
87A TYR* 1.3 70.0 - - - +
89A ASP* 1.3 63.1 + - - +
91A TRP* 3.2 6.5 + + - +
92A GLN* 2.9 53.2 + - + +
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Residues in contact with ASP 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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87A TYR* 3.7 14.4 - - - +
88A HIS* 1.3 76.7 + - - +
90A ILE* 1.3 74.2 + - - +
92A GLN* 3.4 12.5 + - - +
93A MET* 3.5 10.9 + - - +
275A LEU* 3.5 25.1 - - + +
278A LYS* 4.4 5.2 + - - -
279A HIS* 2.6 35.6 + - - -
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Residues in contact with ILE 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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72A LEU* 4.7 0.7 - - + -
87A TYR* 3.7 28.5 - - + +
88A HIS 3.3 0.2 - - - -
89A ASP* 1.3 80.8 + - - +
91A TRP* 1.3 63.0 + - - +
93A MET* 3.4 6.5 + - - +
94A TYR* 3.4 16.5 + - - +
155A ILE* 3.5 24.2 - - + -
157A GLU* 3.6 20.8 - - + +
158A ALA* 3.7 13.0 - - - +
272A PHE* 3.8 9.2 - - + -
275A LEU* 3.7 16.6 - - + -
276A MET* 3.5 32.1 - - + -
279A HIS* 4.0 17.0 - - + +
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Residues in contact with TRP 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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82A ILE* 4.3 17.7 - - + -
83A PHE* 4.5 5.3 - + - -
85A ILE* 3.7 50.0 - - + +
87A TYR 2.9 18.4 + - - +
88A HIS* 3.2 4.5 + + - +
90A ILE* 1.3 76.5 - - - +
92A GLN* 1.3 73.7 + - - +
94A TYR* 3.0 35.7 + + + +
95A LYS* 3.0 50.2 + - + +
156A THR* 5.7 0.9 - - + -
157A GLU* 3.8 19.5 - - + +
160A CYS* 3.9 18.2 - - - -
170B ASN 6.0 0.2 - - - -
174B GLU* 3.4 29.3 + - + -
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Residues in contact with GLN 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 HIS* 2.9 46.5 + - + +
89A ASP* 3.4 6.0 + - - +
90A ILE 3.3 0.2 - - - -
91A TRP* 1.3 91.9 - - - +
93A MET* 1.3 58.8 + - + +
95A LYS* 3.3 16.7 + - - +
96A LYS* 2.9 27.2 + - - +
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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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89A ASP 3.5 8.6 + - - +
90A ILE 3.4 9.3 + - - +
91A TRP 3.1 0.6 - - - -
92A GLN* 1.3 77.5 - - + +
94A TYR* 1.3 59.8 + - - +
96A LYS* 3.3 10.9 + - + +
97A ALA 2.9 23.6 + - - -
161A PHE* 3.5 17.7 - - + -
268A LEU* 3.6 26.3 - - + +
271A ASP* 3.5 19.7 - - + -
272A PHE* 3.3 40.4 - - + +
275A LEU* 3.7 26.7 - - + -
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Residues in contact with TYR 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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82A ILE* 6.2 0.2 - - + -
90A ILE 3.4 7.2 + - - +
91A TRP* 3.0 51.0 + + - +
93A MET* 1.3 77.2 - - - +
95A LYS* 1.3 65.3 + - + +
97A ALA* 3.3 1.7 + - + +
98A GLU* 2.9 49.7 + - + +
157A GLU 4.4 5.6 - - - +
160A CYS* 3.7 37.0 - - + -
161A PHE* 3.7 22.5 - - + +
164A PHE* 4.0 24.7 - + + -
167B ALA* 4.7 1.2 + - - -
170B ASN* 4.3 12.4 - - + +
171B ILE* 3.7 23.6 + - - +
174B GLU* 4.5 4.5 + - - -
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Residues in contact with LYS 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 TRP* 3.0 52.2 + - + +
92A GLN* 3.6 18.6 - - - +
93A MET 3.2 0.4 - - - -
94A TYR* 1.3 78.2 - - + +
96A LYS* 1.3 58.5 + - - +
98A GLU* 3.1 27.6 + - - +
99A ALA* 2.9 30.6 + - - +
105B GLU* 2.5 32.2 + - - -
174B GLU* 2.7 26.7 + - - -
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Residues in contact with LYS 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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92A GLN 2.9 17.0 + - - +
93A MET* 3.7 11.7 - - - +
94A TYR 3.1 0.2 - - - -
95A LYS* 1.3 75.1 - - - +
97A ALA* 1.3 67.4 + - - +
99A ALA* 3.2 12.6 + - - +
100A SER* 2.9 19.3 + - - +
268A LEU* 4.1 27.4 - - + +
271A ASP* 5.9 1.0 + - - -
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Residues in contact with ALA 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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93A MET 2.9 14.9 + - - +
94A TYR* 3.5 9.9 - - - +
96A LYS* 1.3 73.9 - - - +
98A GLU* 1.3 58.2 + - - +
100A SER* 2.8 27.0 + - - -
101A PHE 3.4 6.2 + - - -
161A PHE* 4.2 11.9 - - + +
164A PHE* 3.6 28.9 - - + -
165A GLN 6.0 0.4 - - - +
168A MET* 5.7 1.1 - - + +
268A LEU* 3.7 20.7 - - + +
269A HIS* 5.9 2.9 - - - +
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Residues in contact with GLU 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 TYR* 2.9 39.6 + - + +
95A LYS* 3.1 33.8 + - - +
97A ALA* 1.3 75.8 - - - +
99A ALA* 1.3 60.7 + - - +
100A SER 3.4 0.5 + - - -
101A PHE* 3.6 15.8 + - - +
164A PHE* 3.6 19.4 - - + -
101B PHE* 4.4 6.8 - - + -
103B THR* 3.4 35.9 - - + +
104B ALA 4.7 0.2 + - - -
105B GLU* 4.3 1.9 - - - +
171B ILE* 3.3 27.6 - - - +
174B GLU* 4.0 5.5 - - - +
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Residues in contact with ALA 99 (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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95A LYS 2.9 18.4 + - - +
96A LYS* 3.2 8.0 + - - +
98A GLU* 1.3 76.7 - - - +
100A SER* 1.3 58.8 + - - +
101A PHE* 3.5 1.5 + - - +
103B THR* 5.9 1.3 - - - -
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Residues in contact with SER 100 (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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96A LYS* 2.9 14.6 + - - +
97A ALA* 2.8 17.3 + - - -
99A ALA* 1.3 80.2 - - - +
101A PHE* 1.3 66.6 + - - +
102A TRP* 3.2 18.2 - - - +
168A MET* 5.8 0.4 - - - -
264A ARG* 3.3 36.1 + - - +
265A ASP* 4.6 3.8 + - - +
268A LEU* 5.0 3.3 - - - +
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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