Contacts of the helix formed by residues 87 - 103 (chain A) in PDB entry 2VUU
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 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 4.0 12.4 - - + +
86A GLY* 1.3 64.6 - - - -
88A GLU* 1.3 57.3 + - - +
89A ILE* 2.9 26.8 + - - +
90A ALA* 2.9 24.6 + - + +
91A ILE* 3.0 25.3 + - - +
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 2.9 38.9 + - - +
82A THR 3.7 14.8 - - - +
83A SER* 3.4 25.6 + - - -
86A GLY 2.6 9.1 + - - +
87A ASP* 1.3 70.4 + - - +
89A ILE* 1.3 57.4 + - - +
91A ILE* 4.2 5.5 - - - +
92A GLY* 3.1 22.2 + - - -
110A TYR* 4.4 1.0 + - - +
127A MET* 4.8 10.2 - - - +
130A PRO* 4.6 18.6 - - + +
131A LYS* 3.0 38.7 + - + +
134A VAL* 3.6 7.0 - - + +
1353A NAP 4.0 1.1 + - - -
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP* 2.9 9.4 + - - +
88A GLU* 1.3 75.1 - - - +
90A ALA* 1.3 62.9 + - - +
91A ILE 3.1 1.6 - - - -
93A LYS* 2.9 47.9 + - + +
130A PRO* 3.4 46.2 - - + +
133A THR* 3.7 30.3 - - + +
134A VAL* 3.7 10.2 - - + +
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Residues in contact with ALA 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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61A LEU* 4.9 9.2 - - + -
62A ASN* 5.5 4.0 - - - +
87A ASP* 2.9 30.3 + - + +
89A ILE* 1.3 77.8 - - - +
91A ILE* 1.3 58.3 + - - +
93A LYS* 3.9 5.4 - - - +
94A ASP* 3.0 39.6 + - - +
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Residues in contact with ILE 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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60A LEU* 3.9 28.3 - - + +
61A LEU* 3.9 36.3 - - + +
62A ASN 5.2 0.7 - - - +
67A MET* 4.0 2.6 - - + +
81A THR* 3.9 17.0 - - + -
82A THR 5.5 0.9 - - - +
85A ALA* 3.6 40.4 - - + +
86A GLY 4.3 3.1 - - - +
87A ASP 3.0 18.6 + - - +
88A GLU* 4.2 4.5 - - + +
90A ALA* 1.3 74.7 - - - +
92A GLY* 1.3 66.2 + - - +
93A LYS 3.1 1.5 + - - -
94A ASP* 3.2 7.2 + - - +
95A LEU* 3.0 29.5 + - + +
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Residues in contact with GLY 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 5.1 1.3 - - - -
88A GLU 3.1 15.2 + - - -
89A ILE 3.4 0.4 + - - -
91A ILE* 1.3 80.2 - - - +
93A LYS* 1.3 58.6 + - - +
95A LEU* 3.9 14.2 - - - +
96A ALA* 3.4 19.6 + - - +
108A TYR* 4.3 2.9 + - - -
110A TYR* 4.8 5.6 - - - -
134A VAL* 3.3 31.4 - - - +
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Residues in contact with LYS 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 ILE* 2.9 36.7 + - + +
90A ALA* 3.9 6.7 - - - +
92A GLY* 1.3 75.2 - - - +
94A ASP* 1.3 62.9 + - - +
95A LEU 3.2 0.2 - - - -
96A ALA 3.3 0.9 + - - -
97A ASP* 2.9 36.5 + - - +
133A THR* 5.8 4.3 - - - -
134A VAL* 5.4 2.5 - - + -
137A TYR* 3.5 56.1 - - + +
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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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60A LEU 5.1 0.7 - - - +
62A ASN* 4.6 19.4 + - - +
63A ASN 5.1 0.9 + - - -
64A VAL* 4.4 20.7 - - + +
67A MET* 3.5 21.7 - - + +
90A ALA* 3.0 22.8 + - - +
91A ILE* 3.2 5.3 + - - +
93A LYS* 1.3 78.9 - - - +
95A LEU* 1.3 52.1 + - - +
97A ASP* 3.2 12.2 + - - +
98A ALA* 2.8 34.3 + - - +
101A ARG* 4.4 2.4 + - - -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.8 26.0 - - + -
60A LEU* 4.2 2.7 - - + -
67A MET* 3.3 28.0 - - + -
70A LEU* 4.9 2.5 - - + -
71A PHE* 3.3 24.7 - - + -
79A ILE* 3.5 28.3 - - + -
81A THR* 4.0 9.6 - - + -
91A ILE* 3.0 34.4 + - + +
92A GLY* 3.9 7.6 - - - +
94A ASP* 1.3 79.0 - - - +
96A ALA* 1.3 56.9 + - - +
98A ALA* 3.2 1.8 + - - -
99A ALA* 2.9 27.4 + - - +
108A TYR* 3.7 10.8 - - - +
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Residues in contact with ALA 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 GLY 3.4 15.5 + - - +
93A LYS 3.3 4.8 + - - +
95A LEU* 1.3 79.8 - - - +
97A ASP* 1.3 57.8 + - - +
99A ALA* 4.3 0.2 - - - -
100A LYS* 3.1 20.8 + - - +
108A TYR* 3.6 8.7 + - - +
137A TYR* 4.1 5.2 - - + -
138A VAL* 4.0 23.1 - - + -
141A LEU* 3.5 23.7 - - + +
143A LEU* 3.4 17.9 - - + +
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Residues in contact with ASP 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 LYS* 2.9 18.5 + - - +
94A ASP* 3.4 14.8 - - - +
96A ALA* 1.3 74.5 - - - +
98A ALA* 1.3 66.3 + - - +
100A LYS* 3.2 4.3 + - - +
101A ARG* 2.9 44.7 + - + +
137A TYR* 2.6 32.0 + - - -
141A LEU* 3.4 11.3 - - - +
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Residues in contact with ALA 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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67A MET* 3.7 24.0 - - + +
68A ASP* 4.2 6.7 - - - +
71A PHE* 3.3 22.7 - - + +
94A ASP 2.8 13.2 + - - +
95A LEU 3.3 9.6 - - - +
97A ASP* 1.3 76.0 - - - +
99A ALA* 1.3 63.8 + - - +
101A ARG* 3.0 20.7 + - - +
102A ALA* 2.9 22.0 + - - +
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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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71A PHE* 3.5 18.3 - - + -
95A LEU 2.9 15.9 + - - +
96A ALA 3.7 4.5 - - - +
98A ALA* 1.3 76.3 - - - +
100A LYS* 1.3 62.8 + - - +
102A ALA* 3.2 12.5 + - - +
103A GLY* 3.3 8.3 + - - -
105A ILE* 3.5 21.7 + - + +
108A TYR* 3.6 31.0 - - + -
143A LEU* 4.2 5.6 - - + -
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Residues in contact with LYS 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 ALA 3.1 17.8 + - - +
97A ASP* 3.7 6.5 - - - +
98A ALA 3.2 0.4 - - - -
99A ALA* 1.3 76.7 - - - +
101A ARG* 1.3 64.7 + - + +
103A GLY* 3.0 15.9 + - - -
141A LEU* 3.0 56.8 + - + +
143A LEU* 3.7 18.3 - - + +
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Residues in contact with ARG 101 (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 VAL* 3.0 30.4 - - - +
68A ASP* 2.6 34.4 + - - +
94A ASP 4.4 1.6 + - - -
97A ASP* 2.9 59.8 + - + +
98A ALA* 3.0 16.3 + - - +
100A LYS* 1.3 77.3 - - + +
102A ALA* 1.3 62.6 + - - +
103A GLY* 3.2 1.9 + - - -
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Residues in contact with ALA 102 (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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68A ASP 5.9 0.2 - - - +
71A PHE* 3.8 34.3 - - + +
72A GLU* 5.6 1.1 - - - -
98A ALA 2.9 12.6 + - - +
99A ALA* 3.4 10.8 - - - +
100A LYS 3.2 0.2 - - - -
101A ARG* 1.3 76.5 - - - +
103A GLY* 1.3 58.4 + - - +
104A THR* 3.0 24.6 + - - +
105A ILE* 4.6 2.7 - - + -
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Residues in contact with GLY 103 (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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99A ALA 3.3 3.8 + - - -
100A LYS* 3.0 17.0 + - - -
101A ARG 3.1 1.5 - - - -
102A ALA* 1.3 76.5 - - - +
104A THR* 1.3 61.1 + - - +
105A ILE 3.6 4.4 - - - +
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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