Contacts of the helix formed by residues 73 - 89 (chain A) in PDB entry 2V32
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 ASN 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASP* 1.3 79.5 - - - +
74A VAL* 1.3 62.5 + - - +
75A ALA* 3.0 11.5 + - - +
76A ASP* 2.7 49.0 + - - +
77A HIS* 3.2 17.7 + - - -
100A ALA* 4.1 0.9 - - - -
102A GLU* 3.6 32.2 + - - +
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Residues in contact with VAL 74 (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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15A ASP* 3.7 22.7 - - + +
16A SER 3.6 32.5 - - - +
17A THR* 3.9 11.7 - - + -
73A ASN* 1.3 74.6 - - - +
75A ALA* 1.3 67.2 + - - +
77A HIS* 3.2 7.8 + - - +
78A LYS* 3.0 47.3 + - + +
100A ALA* 3.9 16.8 - - + +
102A GLU* 4.7 1.7 + - - +
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.0 11.0 + - - +
74A VAL* 1.3 80.0 - - - +
76A ASP* 1.3 65.9 + - - +
78A LYS* 3.4 6.4 + - - +
79A GLU* 3.1 22.9 + - - +
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Residues in contact with ASP 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 3.4 13.0 - - + +
41A PHE* 3.8 25.3 - - + -
72A ASP* 4.3 15.3 - - + +
73A ASN* 2.7 35.4 + - - +
75A ALA* 1.3 71.7 - - - +
77A HIS* 1.3 58.8 + - - +
79A GLU* 3.3 6.6 + - - +
80A TRP* 2.8 35.3 + - - +
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Residues in contact with HIS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.4 18.8 - - + -
40A ASP* 2.4 40.8 + - - -
70A SER* 3.2 21.4 + - - -
72A ASP* 3.5 19.3 + - + +
73A ASN 3.2 9.3 + - - -
74A VAL* 3.2 9.5 + - - +
76A ASP* 1.3 74.9 - - - +
78A LYS* 1.3 53.3 + - - +
80A TRP* 4.1 1.0 - - - +
81A SER* 2.6 39.3 + - - -
98A ILE* 3.4 36.9 + - + +
99A ILE 2.8 33.6 - - - -
100A ALA* 3.6 4.5 + - - +
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Residues in contact with LYS 78 (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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16A SER 5.3 0.2 + - - -
17A THR* 3.4 42.2 + - + +
74A VAL* 3.0 30.4 + - - +
75A ALA* 3.8 7.2 - - - +
76A ASP 3.3 0.2 - - - -
77A HIS* 1.3 73.9 - - - +
79A GLU* 1.3 66.8 + - - +
81A SER* 3.4 17.7 - - - -
82A GLU* 3.8 11.4 + - - +
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Residues in contact with GLU 79 (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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41A PHE* 3.3 25.3 - - + -
75A ALA 3.1 16.3 + - - +
76A ASP* 4.5 6.1 - - - +
78A LYS* 1.3 75.6 - - - +
80A TRP* 1.3 63.0 + - - +
82A GLU* 3.2 22.5 + - - +
83A ASP* 4.0 4.2 + - - +
208B SER* 3.7 25.8 - - - +
210B LYS* 4.4 9.8 + - - -
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Residues in contact with TRP 80 (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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37A HIS* 3.2 38.1 - + - -
40A ASP* 3.2 18.8 - - + -
41A PHE* 3.2 48.0 - + + +
42A THR 4.2 0.7 - - - -
45A SER* 3.8 12.3 - - - -
46A THR* 3.0 40.3 + - - -
49A LEU* 3.5 28.7 - - + -
76A ASP 2.8 19.1 + - - +
77A HIS 4.9 3.4 - - - -
79A GLU* 1.3 71.5 - - - +
81A SER* 1.3 68.3 + - - +
82A GLU 3.1 2.5 - - - -
83A ASP* 2.9 15.7 + - + +
84A VAL* 2.9 27.5 + - + +
98A ILE* 4.9 6.7 - - + -
212B TYR* 3.2 18.6 + - - -
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 5.0 2.8 - - - +
77A HIS 2.6 25.7 + - - -
78A LYS* 3.4 12.2 - - - -
80A TRP* 1.3 79.0 - - - +
82A GLU* 1.4 56.6 + - - +
84A VAL* 3.2 12.4 + - - +
85A LYS* 2.9 37.0 + - - +
94A MET* 3.7 25.0 - - - +
98A ILE* 3.6 19.8 - - - +
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Residues in contact with GLU 82 (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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78A LYS 4.2 9.1 - - - +
79A GLU* 3.2 15.1 + - + +
80A TRP 3.0 1.4 + - - -
81A SER* 1.4 74.7 - - - +
83A ASP* 1.3 61.0 + - - +
85A LYS* 2.7 42.5 + - - +
86A CYS* 3.1 26.2 + - - +
207B PRO* 3.9 20.0 - - + +
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Residues in contact with ASP 83 (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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41A PHE* 3.8 6.1 - - - -
46A THR* 4.0 3.4 - - + +
79A GLU 4.6 1.8 - - - +
80A TRP* 2.9 13.7 + - + +
82A GLU* 1.3 74.9 - - - +
84A VAL* 1.3 65.4 + - - +
86A CYS* 3.3 7.0 + - - +
87A LEU* 3.1 24.9 + - - +
206B VAL* 3.7 14.9 - - + +
207B PRO* 3.4 10.2 - - - +
208B SER* 2.8 49.5 + - - -
212B TYR* 2.7 33.6 + - - +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 4.0 11.4 - - + -
49A LEU* 3.6 41.7 - - + +
50A GLY* 3.6 2.1 - - - +
53A ILE* 3.7 12.8 - - + -
80A TRP* 2.9 58.4 + - + +
81A SER* 3.2 11.2 + - - +
83A ASP* 1.3 78.2 - - - +
85A LYS* 1.3 55.7 + - - +
87A LEU* 3.4 2.3 + - - +
88A SER* 3.0 27.9 + - - -
94A MET* 4.1 9.0 - - + -
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 4.2 7.0 - - + -
81A SER* 2.9 20.2 + - - +
82A GLU* 2.7 41.3 + - - +
83A ASP 3.3 0.2 - - - -
84A VAL* 1.3 69.7 - - - +
86A CYS* 1.3 69.4 + - - +
88A SER* 2.7 24.1 + - - -
89A GLY* 3.2 3.6 + - - -
90A VAL 3.6 15.1 + - - +
91A LYS* 6.0 0.2 - - - -
92A GLY 3.6 27.5 + - - +
93A ASP* 4.3 10.3 + - - +
94A MET* 3.8 35.6 - - - +
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Residues in contact with CYS 86 (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 GLU 3.1 12.7 + - - +
83A ASP 3.4 9.4 - - - +
85A LYS* 1.3 83.6 - - - +
87A LEU* 1.3 62.8 + - - +
89A GLY* 3.1 10.4 + - - -
204B LYS* 5.1 9.6 - - - -
205B ALA 4.7 11.2 - - - -
206B VAL* 5.0 3.8 - - + -
207B PRO* 3.9 27.1 - - + -
200C ASN* 3.3 12.4 + - - +
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Residues in contact with LEU 87 (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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46A THR* 3.7 25.8 - - + +
47A THR* 3.9 33.4 - - + +
50A GLY* 5.0 1.8 - - - -
54A GLN* 4.4 4.9 + - - -
83A ASP 3.1 12.7 + - - +
84A VAL 3.9 3.1 - - - +
86A CYS* 1.3 79.3 - - - +
88A SER* 1.3 60.7 + - - +
204B LYS* 3.6 23.3 - - - +
213B LEU* 3.8 23.6 - - + -
215B TYR* 3.7 13.0 - - - +
200C ASN* 2.9 25.6 + - + +
217C PRO* 5.8 0.3 - - - +
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Residues in contact with SER 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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50A GLY* 3.3 32.4 - - - -
53A ILE* 3.8 16.2 - - - +
54A GLN* 3.3 25.8 + - - +
84A VAL 3.0 14.4 + - - -
85A LYS* 2.7 19.6 + - - -
87A LEU* 1.3 75.7 - - - +
89A GLY* 1.3 56.9 + - - +
90A VAL* 2.9 24.4 + - - +
200C ASN* 3.9 1.3 + - - -
217C PRO* 5.0 3.3 - - - +
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Residues in contact with GLY 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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85A LYS 3.2 1.3 + - - -
86A CYS 3.1 13.9 + - - -
87A LEU 3.1 1.2 - - - -
88A SER* 1.3 76.6 + - - +
90A VAL* 1.3 60.7 + - - +
91A LYS* 4.0 11.0 + - - +
199C PRO* 5.3 9.8 - - - +
200C ASN* 3.5 15.7 - - - -
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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