Contacts of the helix formed by residues 87 - 103 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 3.9 14.6 - - + +
86B GLY* 1.3 67.5 - - - +
88B GLU* 1.3 61.5 + - - +
89B ILE* 3.0 13.7 + - - +
90B ALA* 2.7 43.8 + - + +
91B ILE* 3.1 24.4 + - - +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B THR* 2.8 20.8 + - - +
82B THR* 3.2 24.9 - - - +
83B SER* 3.7 20.9 + - - -
86B GLY 2.9 5.4 + - - +
87B ASP* 1.3 69.1 - - - +
89B ILE* 1.3 61.6 + - - +
91B ILE* 4.6 3.8 - - + -
92B GLY* 3.0 25.3 + - - -
110B TYR* 4.3 5.0 + - - +
126B PRO 5.3 0.2 - - - +
127B MET* 3.9 15.5 - - - +
130B PRO* 4.6 20.9 - - + +
131B LYS* 2.6 44.0 + - - +
134B VAL* 3.5 5.9 - - - +
1353B NAP 4.6 1.5 + - - -
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ASP* 3.0 7.8 + - - +
88B GLU* 1.3 75.4 - - - +
90B ALA* 1.3 56.0 + - - +
92B GLY* 3.0 2.3 + - - -
93B LYS* 2.7 65.8 + - + +
130B PRO* 3.9 34.3 - - + +
133B THR* 4.2 24.0 - - + +
134B VAL* 3.5 7.6 - - + +
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.6 9.4 - - + -
62B ASN* 5.4 6.5 - - - +
87B ASP* 2.7 36.9 + - + +
89B ILE* 1.3 75.1 - - - +
91B ILE* 1.3 60.2 + - - +
93B LYS* 4.1 5.4 - - - +
94B ASP* 3.1 33.4 + - - +
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Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.8 30.1 - - + -
61B LEU* 3.6 39.0 - - + +
62B ASN 5.0 0.7 - - - +
67B MET* 4.3 3.4 - - + -
81B THR* 4.4 9.0 - - + -
82B THR 5.6 0.7 - - - +
85B ALA* 3.7 35.7 - - + +
86B GLY 3.9 3.4 - - - +
87B ASP 3.1 19.5 + - - +
88B GLU* 4.3 4.0 - - - +
90B ALA* 1.3 75.2 - - - +
92B GLY* 1.3 61.1 + - - +
94B ASP* 3.0 7.1 + - - +
95B LEU* 2.9 43.7 + - + +
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Residues in contact with GLY 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B THR* 4.9 2.9 - - - +
88B GLU 3.0 19.0 + - - -
89B ILE 3.0 3.6 + - - -
91B ILE* 1.3 77.6 - - - +
93B LYS* 1.3 58.6 + - - +
95B LEU* 3.8 11.1 + - - +
96B ALA* 3.2 20.3 + - - +
108B TYR* 4.2 2.6 + - - -
110B TYR* 4.5 6.5 - - - -
134B VAL* 3.5 27.7 - - - +
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 2.7 42.9 + - + +
90B ALA* 4.1 6.1 - - - +
92B GLY* 1.3 71.2 - - - +
94B ASP* 1.3 69.8 + - - +
96B ALA* 3.4 2.3 + - - +
97B ASP* 3.0 33.0 + - - +
133B THR* 5.1 8.6 - - - +
134B VAL* 4.7 2.9 - - + -
137B TYR* 3.6 53.6 - - + -
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASN* 4.5 18.9 + - - +
64B VAL* 4.2 20.6 - - + +
67B MET* 3.4 27.2 - - + +
90B ALA* 3.1 20.3 + - - +
91B ILE* 3.0 1.4 + - - +
93B LYS* 1.3 80.9 - - - +
95B LEU* 1.3 52.0 + - - +
97B ASP* 3.0 10.9 + - - +
98B ALA* 2.7 35.0 + - - +
101B ARG* 4.4 3.1 + - - +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.9 27.6 - - + -
60B LEU* 4.3 4.7 - - + -
67B MET* 3.5 32.7 - - + -
70B LEU* 4.8 2.0 - - + -
71B PHE* 3.2 25.3 - - + -
79B ILE* 3.6 28.9 - - + -
81B THR* 4.1 8.1 - - + -
91B ILE* 2.9 34.5 + - + +
92B GLY* 3.9 4.0 - - - +
94B ASP* 1.3 77.3 - - - +
96B ALA* 1.3 56.4 + - - +
98B ALA 3.1 0.5 + - - -
99B ALA* 2.9 27.5 + - - +
108B TYR* 3.8 11.0 - - - +
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLY 3.2 16.7 + - - +
93B LYS 3.7 4.0 - - - +
94B ASP 3.3 0.2 - - - -
95B LEU* 1.3 79.2 - - - +
97B ASP* 1.3 56.7 + - - +
100B LYS* 3.0 22.0 + - - +
108B TYR* 3.4 16.5 + - - +
137B TYR* 3.9 11.7 - - + -
138B VAL* 4.2 10.1 - - + -
141B LEU* 3.3 28.2 - - + +
143B LEU* 3.6 12.1 - - + +
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Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LYS* 3.0 21.9 + - - +
94B ASP* 3.0 10.9 + - - +
96B ALA* 1.3 75.5 - - - +
98B ALA* 1.3 60.6 + - - +
100B LYS* 3.2 3.9 + - - +
101B ARG* 2.9 49.1 + - - +
137B TYR* 2.4 35.8 + - - -
141B LEU* 3.3 11.7 - - - +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B MET* 3.7 22.7 - - + +
68B ASP* 4.0 7.9 - - - +
71B PHE* 3.4 27.0 - - + +
94B ASP 2.7 19.0 + - - +
97B ASP* 1.3 73.8 - - - +
99B ALA* 1.3 55.2 + - - +
101B ARG* 3.2 23.5 + - - +
102B ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.5 23.0 - - + -
95B LEU 2.9 16.2 + - - +
96B ALA 3.8 2.9 - - - +
98B ALA* 1.3 74.9 - - - +
100B LYS* 1.3 65.1 + - - +
102B ALA* 3.4 11.3 + - - +
103B GLY* 3.4 8.5 + - - -
105B ILE* 3.8 19.8 - - + +
108B TYR* 3.5 31.6 - - + -
143B LEU* 4.5 4.0 - - + -
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ALA 3.0 18.1 + - - +
97B ASP* 3.2 5.6 + - - +
99B ALA* 1.3 73.5 - - - +
101B ARG* 1.3 66.3 + - - +
103B GLY* 3.0 16.4 + - - -
141B LEU* 3.0 55.4 + - + +
142B GLY 5.2 1.8 + - - -
143B LEU* 3.7 19.0 - - + +
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B VAL* 3.7 25.8 - - - +
68B ASP* 3.1 22.9 + - - +
94B ASP* 4.4 2.8 + - - +
97B ASP* 2.9 28.4 + - - +
98B ALA* 3.3 30.6 - - - +
100B LYS* 1.3 77.7 - - - +
102B ALA* 1.3 62.6 + - - +
103B GLY* 3.2 1.4 + - - -
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASP 5.9 0.2 - - - +
71B PHE* 3.6 28.0 - - + +
72B GLU* 5.6 1.1 - - - -
98B ALA 2.9 12.0 + - - +
99B ALA* 3.5 10.8 - - - +
100B LYS 3.2 0.2 - - - -
101B ARG* 1.3 75.8 - - - +
103B GLY* 1.3 57.6 + - - +
104B THR* 3.0 30.8 + - - +
105B ILE* 5.0 2.5 - - + -
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ALA 3.4 4.5 + - - -
100B LYS* 3.0 17.7 + - - -
101B ARG 3.1 1.5 - - - -
102B ALA* 1.3 75.9 - - - +
104B THR* 1.3 60.2 + - - +
105B 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