Contacts of the helix formed by residues 57 - 70 (chain A) in PDB entry 3B4V
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 SER 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A SER 4.3 0.4 + - - -
56A LEU* 1.3 72.6 - - - +
58A PHE* 1.3 59.6 + - - +
59A HIS* 3.5 6.4 + - - +
60A SER* 3.3 25.1 + - - -
61A THR* 2.7 29.6 + - - -
84A THR* 6.3 2.7 - - - -
115A CYS 5.3 1.3 + - - -
86B LEU* 4.5 8.2 - - - +
107B ASN* 4.1 23.3 + - - +
24D LEU* 5.4 5.3 - - - +
60D PHE* 3.4 4.9 - - - -
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Residues in contact with PHE 58 (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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57A SER* 1.3 73.6 - - - +
59A HIS* 1.3 59.1 + - - +
61A THR* 3.4 3.1 + - - -
62A VAL* 3.0 37.5 + - + +
20B PHE* 3.9 11.9 - + - -
25B TRP* 3.7 19.2 - + - -
35B TYR* 3.4 28.5 - + - -
91B MET* 3.9 17.5 - - + -
105B ILE* 3.9 21.5 - - + -
106B GLN 3.9 9.6 - - - +
107B ASN* 3.3 12.9 + - + +
108B MET* 3.6 29.2 - - + -
57D LEU* 4.1 11.4 - - + -
60D PHE* 3.4 38.7 - + + -
61D LEU* 5.5 0.4 - - + -
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Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER* 3.3 4.8 + - - +
58A PHE* 1.3 73.5 - - - +
60A SER* 1.3 66.0 + - - +
62A VAL* 3.3 6.5 + - - +
63A ILE* 2.9 46.8 + - + +
116A SER* 5.7 1.9 + - - -
37B ALA* 2.9 21.1 + - + +
38B ASN 2.7 26.9 + - - -
39B TYR* 4.6 3.6 - - + -
83B PRO* 4.5 8.8 - - + +
86B LEU* 4.1 14.4 - - + +
107B ASN 2.9 22.5 + - - +
108B MET 3.2 23.6 - - - +
110B VAL* 3.2 26.1 - - + +
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Residues in contact with SER 60 (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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56A LEU* 3.9 16.7 - - - +
57A SER* 3.3 18.8 + - - -
59A HIS* 1.3 81.1 + - - +
61A THR* 1.3 59.9 + - - +
63A ILE* 3.3 3.8 + - - +
64A ASN* 2.8 30.1 + - - +
67A ARG* 4.8 0.3 + - - -
115A CYS 2.5 29.2 + - - -
116A SER* 3.4 25.3 + - - +
83B PRO* 6.1 0.3 - - - +
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Residues in contact with THR 61 (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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56A LEU* 3.5 16.4 - - + +
57A SER 2.7 18.9 + - - -
58A PHE 3.4 7.9 - - - -
60A SER* 1.3 76.9 - - - +
62A VAL* 1.3 63.0 + - - +
64A ASN* 3.0 3.9 + - + +
65A HIS* 3.0 22.7 + - - +
23B ILE* 6.3 0.2 - - - -
25B TRP* 3.7 27.8 - - + -
53D ASN* 3.8 22.7 + - + +
56D ASN* 3.5 16.5 + - - +
60D PHE* 3.4 16.4 - - + -
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Residues in contact with VAL 62 (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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58A PHE* 3.0 40.5 + - + +
59A HIS 3.5 8.5 - - - +
61A THR* 1.3 78.5 - - - +
63A ILE* 1.3 65.9 + - + +
65A HIS* 3.4 7.6 + - - +
66A TYR* 3.3 21.7 - - - -
18B VAL* 3.3 38.4 - - + -
20B PHE* 5.0 0.4 - - + -
23B ILE* 3.7 22.2 - - + -
25B TRP* 3.9 11.0 - - + -
35B TYR* 4.0 4.0 - - + +
37B ALA* 4.1 14.1 - - + -
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Residues in contact with ILE 63 (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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59A HIS* 2.9 41.0 + - + +
60A SER* 3.8 5.6 - - - +
62A VAL* 1.3 82.5 - - + +
64A ASN* 1.3 57.9 + - - +
66A TYR* 2.9 23.4 + - - +
67A ARG* 3.0 36.8 + - - +
74A PHE* 4.1 26.9 - - + -
77A LEU* 4.5 7.6 - - + -
116A SER* 4.4 5.2 - - - +
16B PHE* 4.6 13.7 - - + -
37B ALA* 5.1 1.1 - - + -
38B ASN 3.8 18.8 - - - +
39B TYR* 4.0 11.9 - - + -
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Residues in contact with ASN 64 (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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45A PRO* 3.7 26.5 - - - +
46A SER 5.3 1.7 - - - +
56A LEU* 3.8 17.5 - - + +
60A SER 2.8 21.1 + - - +
61A THR* 3.0 6.3 + - + +
63A ILE* 1.3 70.0 - - - +
65A HIS* 1.3 65.4 + - - +
67A ARG* 2.9 32.9 + - - +
68A MET* 2.8 53.9 + - + +
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Residues in contact with HIS 65 (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 THR 3.0 10.3 + - - +
62A VAL 3.5 11.9 - - - +
63A ILE 3.2 0.2 - - - -
64A ASN* 1.3 75.8 - - - +
66A TYR* 1.3 77.5 + + - +
68A MET* 3.5 15.9 + - + +
69A ARG* 3.3 59.8 + - + +
71A HIS* 5.3 2.0 - - - -
22B ASP* 3.2 39.8 + - + -
23B ILE* 3.6 33.1 + - + +
53D ASN* 4.4 16.1 - - - +
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Residues in contact with TYR 66 (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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62A VAL 3.3 17.0 - - - -
63A ILE* 2.9 8.7 + - - +
65A HIS* 1.3 91.6 - + - +
67A ARG* 1.3 66.6 + - - +
69A ARG 3.6 0.5 + - - -
70A GLY 3.2 16.8 + - - -
71A HIS* 3.5 39.8 + + + -
74A PHE* 3.7 25.5 - + + +
16B PHE* 3.8 30.2 - + - -
17B PHE 4.7 0.7 + - - -
18B VAL* 3.8 21.0 - - + -
19B SER* 3.5 24.9 + - - -
22B ASP* 3.9 20.6 + - + +
23B ILE* 4.2 6.7 - - + +
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Residues in contact with ARG 67 (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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45A PRO* 4.7 7.4 - - - +
46A SER 5.5 6.5 - - - +
56A LEU* 5.9 0.4 - - - +
60A SER 4.8 0.4 + - - -
63A ILE* 3.0 28.2 + - + +
64A ASN* 2.9 45.5 + - - +
66A TYR* 1.3 76.7 - - - +
68A MET* 1.3 60.3 + - + +
70A GLY* 3.3 13.2 + - - -
74A PHE* 3.5 27.8 - - + +
75A ALA* 5.2 2.8 - - - +
77A LEU* 3.0 30.7 + - - +
78A LYS* 4.4 3.5 + - - +
79A SER* 3.9 31.6 - - - +
116A SER* 3.2 29.7 + - - -
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Residues in contact with MET 68 (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 SER 5.3 8.5 - - - +
64A ASN* 2.8 48.7 + - + +
65A HIS* 4.0 18.2 - - + +
67A ARG* 1.3 74.3 - - + +
69A ARG* 1.3 61.9 + - + +
70A GLY* 3.6 0.9 + - - -
53D ASN* 5.0 12.1 - - + +
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Residues in contact with ARG 69 (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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65A HIS* 3.3 49.6 + - + +
66A TYR 3.6 0.2 + - - -
68A MET* 1.3 79.1 - - + +
70A GLY* 1.3 61.4 + - - +
71A HIS* 3.5 32.4 + - + +
22B ASP 5.3 1.5 + - - -
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Residues in contact with GLY 70 (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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66A TYR 3.2 5.6 + - - -
67A ARG 3.3 10.3 + - - -
68A MET 3.3 3.6 - - - -
69A ARG* 1.3 78.9 - - - +
71A HIS* 1.3 67.0 + - - +
75A ALA* 4.1 18.6 - - - +
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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