Contacts of the helix formed by residues 53 - 72 (chain A) in PDB entry 2H31
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 LYS 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY* 1.3 76.9 - - - +
54A ALA* 1.3 68.4 + - - +
55A ALA* 3.1 4.7 - - - +
56A ILE* 3.2 27.7 + - + +
57A SER* 3.4 10.5 + - - -
212A ASP* 4.4 14.8 + - - -
249A PHE* 3.4 59.3 - - + +
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Residues in contact with ALA 54 (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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36A LYS* 3.5 43.2 - - + +
53A LYS* 1.3 78.9 - - - +
55A ALA* 1.3 60.6 + - - +
56A ILE 3.2 0.2 - - - -
57A SER* 3.4 11.1 + - - -
58A ASN* 3.2 21.1 + - - +
84A THR* 4.1 9.3 - - + +
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 3.1 1.7 - - - +
54A ALA* 1.3 75.8 - - - +
56A ILE* 1.3 66.3 + - + +
58A ASN 3.4 0.6 + - - -
59A LYS* 3.1 22.0 + - - +
83A GLU* 3.6 28.0 - - + +
84A THR* 3.5 24.2 - - + +
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 3.2 23.9 + - + +
55A ALA* 1.3 79.1 - - + +
57A SER* 1.3 65.6 + - - +
59A LYS* 2.9 23.5 + - + +
60A ILE* 2.9 24.0 + - + +
249A PHE* 3.6 39.9 - - + +
250A GLU* 5.5 2.7 - - + -
253A ALA* 3.5 26.2 - - + -
254A GLU* 6.3 0.4 - - + -
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 3.6 14.5 + - - -
53A LYS* 3.4 10.5 + - - -
54A ALA* 3.5 15.7 - - - -
56A ILE* 1.3 83.1 - - - +
58A ASN* 1.3 55.8 + - - +
60A ILE* 4.1 2.2 - - - -
61A THR* 3.3 26.9 + - - +
208A VAL* 4.3 3.7 - - - +
210A ASP* 2.8 39.7 + - - +
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Residues in contact with ASN 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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34A GLN* 4.4 3.0 + - - +
54A ALA 3.2 13.2 + - - +
55A ALA 3.8 0.2 - - - +
56A ILE 3.0 0.8 - - - -
57A SER* 1.3 75.6 - - - +
59A LYS* 1.3 58.6 + - - +
60A ILE 3.3 0.2 - - - -
61A THR* 3.3 3.9 - - - +
62A SER* 2.7 43.0 + - - -
80A LYS* 3.8 6.7 - - - -
83A GLU 3.5 19.3 - - - +
84A THR* 3.7 5.3 + - - -
85A ALA* 2.9 43.7 + - - +
86A PHE* 3.5 27.1 - - - -
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Residues in contact with LYS 59 (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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55A ALA 3.1 13.6 + - - +
56A ILE* 2.9 15.1 + - + +
58A ASN* 1.3 74.2 - - - +
60A ILE* 1.3 68.0 + - - +
62A SER* 3.4 2.5 + - - -
63A CYS* 3.4 26.1 + - - -
80A LYS* 4.3 21.5 - - - +
253A ALA* 2.9 43.1 - - + +
254A GLU* 4.7 6.4 - - - +
256A VAL* 4.2 2.0 - - + -
257A GLU* 3.4 38.3 + - - +
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 2.9 29.3 + - + +
57A SER* 4.1 5.8 - - - +
59A LYS* 1.3 78.3 - - + +
61A THR* 1.3 63.2 + - - +
62A SER 3.0 1.1 + - - -
63A CYS* 3.1 3.5 + - - +
64A ILE* 3.1 25.5 + - + +
209A ILE 3.4 17.0 - - - +
210A ASP* 3.9 13.0 - - - -
211A ASN* 4.6 5.2 - - + +
214A TRP* 4.3 15.3 - - + -
249A PHE 5.2 0.7 - - - +
252A VAL* 3.8 6.5 - - + +
253A ALA* 3.3 36.8 - - + +
256A VAL* 3.5 33.9 - - + -
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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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57A SER 3.3 15.9 + - - +
58A ASN* 3.3 15.3 - - - +
60A ILE* 1.3 80.8 - - - +
62A SER* 1.3 59.8 + - - +
63A CYS 3.4 0.2 - - - -
64A ILE* 4.8 2.2 - - - +
65A PHE* 3.2 34.8 + - - +
86A PHE* 3.6 31.6 - - + -
208A VAL* 3.0 20.2 - - + -
209A ILE 2.6 33.2 + - - +
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Residues in contact with SER 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 2.7 26.2 + - - -
59A LYS* 3.7 5.6 - - - -
60A ILE 3.0 0.6 - - - -
61A THR* 1.3 79.8 - - - +
63A CYS* 1.3 62.9 + - - +
65A PHE 4.1 0.2 - - - -
66A GLN* 3.2 27.2 + - - +
77A PHE* 3.8 24.4 - - - -
80A LYS* 3.4 35.1 - - - +
86A PHE* 4.2 2.8 - - - +
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Residues in contact with CYS 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 LYS* 3.4 14.8 + - - +
60A ILE 3.1 6.6 + - - +
62A SER* 1.3 77.5 - - - +
64A ILE* 1.3 58.6 + - + +
65A PHE 2.9 1.9 + - - -
66A GLN* 2.9 5.7 + - - +
67A LEU* 2.6 37.5 + - - +
256A VAL* 4.0 23.1 - - + +
257A GLU* 3.8 37.7 - - - -
260A LEU* 4.2 17.2 - - + +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 3.1 19.8 + - + +
61A THR 4.6 1.6 - - - +
63A CYS* 1.3 77.2 - - + +
65A PHE* 1.3 57.3 + - + +
67A LEU* 3.4 7.0 - - + +
68A LEU* 2.8 55.7 + - + +
176A LEU* 3.8 22.9 - - + -
209A ILE* 3.9 28.5 - - + +
214A TRP* 3.4 35.9 - - + -
256A VAL* 4.7 8.3 - - + +
259A LEU* 4.4 18.6 - - + -
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 3.2 22.9 + - - +
62A SER 4.2 0.7 - - - +
63A CYS 3.0 0.8 - - - -
64A ILE* 1.3 81.2 - - + +
66A GLN* 1.3 66.9 + - - +
67A LEU 3.0 1.1 - - - -
68A LEU* 3.2 3.3 + - - +
69A GLN* 2.8 28.7 + - - +
75A THR* 4.1 6.3 + - - +
76A ALA 3.5 16.6 - - - -
77A PHE* 3.3 43.7 - + + -
86A PHE* 3.9 18.2 - + - -
205A LEU* 4.0 31.0 - - + -
206A ALA 5.0 0.2 - - - -
207A ASP* 3.7 7.9 - - - -
208A VAL* 3.6 23.6 - - - -
209A ILE* 3.9 24.2 - - + -
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Residues in contact with GLN 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 SER 3.2 18.3 + - - +
63A CYS* 2.9 6.0 + - - +
65A PHE* 1.3 79.0 - - - +
67A LEU* 1.3 53.4 + - - +
69A GLN* 3.5 7.5 - - - +
70A GLU* 2.8 54.6 + - + +
77A PHE* 4.3 15.6 - - + -
260A LEU* 3.3 32.7 - - + +
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Residues in contact with LEU 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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63A CYS 2.6 21.9 + - - +
64A ILE* 3.4 7.9 - - + +
66A GLN* 1.3 69.9 - - - +
68A LEU* 1.3 66.2 + - + +
70A GLU* 3.2 5.9 + - + +
71A ALA* 3.0 24.0 + - + +
175A ILE* 5.1 3.8 - - + -
176A LEU* 3.9 22.4 - - + -
179A SER* 3.5 30.5 - - - +
259A LEU* 3.0 38.8 - - + +
260A LEU* 3.5 21.0 - - + +
397A LEU* 3.9 17.2 - - + +
400A SER* 5.9 1.1 - - - +
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Residues in contact with LEU 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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64A ILE* 2.8 45.1 + - + +
65A PHE* 3.9 3.4 - - + +
67A LEU* 1.3 73.9 - - + +
69A GLN* 1.3 60.2 + - - +
71A ALA* 3.4 4.6 + - - +
72A GLY 3.2 4.7 + - - -
73A ILE* 2.9 36.1 + - + +
75A THR* 4.2 11.0 - - + -
172A ILE* 3.4 22.9 - - + -
175A ILE* 4.0 23.1 - - + -
176A LEU* 3.4 28.0 - - + -
205A LEU* 3.2 29.6 - - + -
209A ILE* 4.3 1.6 - - + -
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Residues in contact with GLN 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 PHE 2.8 16.5 + - - +
66A GLN* 3.5 6.2 - - - +
68A LEU* 1.3 74.6 - - - +
70A GLU* 1.3 69.7 + - - +
71A ALA 3.1 1.6 - - - -
72A GLY* 3.0 20.1 + - - -
73A ILE 3.8 11.4 - - - +
75A THR* 3.2 27.8 + - - +
77A PHE* 2.9 46.4 + - - +
78A THR 4.4 3.1 - - - +
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Residues in contact with GLU 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 GLN* 2.8 45.4 + - + +
67A LEU* 3.2 5.6 + - - +
69A GLN* 1.3 85.8 - - - +
71A ALA* 1.3 60.9 + - - +
72A GLY* 3.5 0.7 + - - -
260A LEU* 5.5 3.1 - - + -
397A LEU* 6.4 1.8 - - + -
401A LYS* 3.7 24.6 + - - +
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.0 16.7 + - + +
68A LEU* 3.6 8.5 - - - +
69A GLN 3.1 0.2 - - - -
70A GLU* 1.3 79.0 - - - +
72A GLY* 1.3 59.7 + - - +
175A ILE* 4.2 15.0 - - + -
397A LEU 5.5 0.2 - - - -
400A SER* 3.7 31.4 - - - +
401A LYS* 3.4 26.6 - - - +
404A ALA* 3.0 16.3 - - + +
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Residues in contact with GLY 72 (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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69A GLN 3.0 12.9 + - - -
70A GLU 3.2 0.4 - - - -
71A ALA* 1.3 81.4 - - - +
73A ILE* 1.3 66.2 + - - +
74A LYS* 3.5 4.5 + - - +
404A ALA* 3.8 4.7 - - - -
408A ASN* 3.0 26.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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