Contacts of the helix formed by residues 58 - 77 (chain A) in PDB entry 5CXV
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 THR 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU 3.7 19.3 - - - +
56A LEU 2.9 6.7 + - - -
57A LYS* 1.3 78.1 - - - +
59A VAL* 1.3 59.5 + - - +
60A ASN* 3.6 14.1 + - - +
61A ASN* 2.8 42.8 + - - +
62A TYR* 3.0 18.0 + - - -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 1.3 72.7 - - - +
60A ASN* 1.3 64.4 + - - +
62A TYR* 3.1 25.4 + - + +
63A PHE* 3.3 11.4 - - + -
137A ARG* 3.7 52.3 - - - +
138A THR 4.6 0.7 - - - +
139A PRO* 4.0 31.4 - - + -
142A ALA* 3.7 24.0 - - + -
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Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 3.2 12.2 + - - +
59A VAL* 1.3 79.9 - - - +
61A ASN* 1.3 64.1 + - - +
63A PHE* 3.4 17.0 + - - +
64A LEU* 3.7 13.2 + - - +
137A ARG* 3.2 24.6 + - - +
504A PGE 4.1 13.1 + - - +
1C ASP 2.9 37.9 + - - -
2C TYR* 3.7 37.1 + - + +
5C ASP* 5.2 3.0 + - - -
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Residues in contact with ASN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 3.7 12.7 - - + -
56A LEU* 2.6 53.4 + - - +
58A THR* 2.8 23.6 + - - +
60A ASN* 1.3 74.0 - - - +
62A TYR* 1.3 65.6 + - - +
63A PHE 3.3 0.9 - - - -
64A LEU* 3.7 17.0 - - - +
65A LEU* 2.9 24.6 + - - +
422A ASN* 5.4 1.1 + - - +
425A PHE* 3.6 24.8 - - + -
2C TYR* 5.0 2.4 + - - -
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Residues in contact with TYR 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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50A PHE* 3.6 25.1 - + - -
57A LYS* 4.5 6.3 + - - +
58A THR 3.0 33.3 + - - -
59A VAL* 3.1 13.2 + - + +
61A ASN* 1.3 76.3 - - - +
63A PHE* 1.3 62.7 + - - +
65A LEU* 3.1 9.2 + - - +
66A SER* 3.0 18.5 + - - -
139A PRO* 3.4 45.3 - - + +
142A ALA* 3.9 20.4 - - + -
143A ALA* 4.4 8.1 - - + -
146A ILE* 3.6 20.6 - - + +
502A Y01 3.3 48.0 - - + +
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Residues in contact with PHE 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 VAL* 3.3 30.3 - - + -
60A ASN* 3.8 10.1 - - - +
61A ASN 3.3 0.6 - - - -
62A TYR* 1.3 76.8 - - + +
64A LEU* 1.3 58.0 + - + +
66A SER* 3.1 5.4 + - - +
67A LEU* 2.9 28.9 + - - +
115A ASN* 4.2 5.4 - - + +
118A LEU* 3.9 36.3 - - + -
119A ILE* 3.7 31.3 - - + +
122A ASP* 4.1 31.2 - - + -
133A TYR* 5.7 0.4 - - - -
137A ARG* 4.2 7.4 - - - -
142A ALA* 4.5 17.5 - - + -
145A MET* 5.8 6.7 - - + -
146A ILE* 3.9 20.4 - - + -
504A PGE 4.2 10.3 - - - +
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Residues in contact with LEU 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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46A VAL* 4.4 4.7 - - + +
60A ASN 3.7 9.6 + - - +
61A ASN* 3.5 26.8 + - + +
62A TYR 3.4 0.6 - - - -
63A PHE* 1.3 78.0 - - + +
65A LEU* 1.3 56.1 + - - +
67A LEU* 3.8 8.1 - - + +
68A ALA* 2.9 29.3 + - - +
119A ILE* 4.6 16.4 - - + -
366A THR* 6.0 1.8 - - + -
370A ILE* 4.8 7.6 - - + -
418A TYR* 3.6 62.3 + - + -
422A ASN* 6.1 0.7 - - - +
425A PHE* 4.4 6.1 - - + -
504A PGE 5.9 4.9 - - - +
2C TYR* 4.8 11.0 - - - +
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Residues in contact with LEU 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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46A VAL* 4.1 8.2 - - + +
47A LEU* 3.8 35.6 - - + +
50A PHE* 3.5 52.3 - - + -
61A ASN 2.9 17.6 + - - +
62A TYR 3.3 5.8 - - - +
64A LEU* 1.3 75.9 - - - +
66A SER* 1.3 57.5 + - - +
68A ALA* 3.2 5.3 + - - +
69A CYS* 2.9 34.7 + - - -
502A Y01 3.6 29.6 - - + +
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Residues in contact with SER 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 TYR 3.0 10.2 + - - -
63A PHE* 3.1 7.8 + - - -
65A LEU* 1.3 73.1 - - - +
67A LEU* 1.3 63.5 + - - +
69A CYS* 3.0 13.7 + - - +
70A ALA* 3.0 10.4 + - - +
115A ASN* 2.3 26.9 + - - +
146A ILE* 3.4 24.0 - - - +
150A TRP* 2.6 31.2 + - - -
502A Y01 4.0 13.6 - - - +
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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 PHE 2.9 14.7 + - - +
64A LEU* 3.8 16.4 - - + +
66A SER* 1.3 73.9 - - - +
68A ALA* 1.3 58.1 + - - +
70A ALA* 3.1 5.3 + - - +
71A ASP* 2.9 36.3 + - - +
112A SER* 3.8 34.5 - - - +
115A ASN* 3.3 16.9 + - + -
116A LEU* 4.2 21.8 - - + -
119A ILE* 4.3 14.8 - - + -
370A ILE* 4.7 8.5 - - + -
414A ASN* 3.8 33.4 - - + +
418A TYR* 5.3 3.4 - - + +
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Residues in contact with ALA 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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43A ASN* 3.4 28.4 - - + +
46A VAL* 4.0 16.8 - - + -
47A LEU* 3.9 17.3 - - + +
64A LEU 2.9 19.8 + - - +
65A LEU 3.5 5.4 - - - +
66A SER 3.2 0.2 - - - -
67A LEU* 1.3 75.9 - - - +
69A CYS* 1.3 57.4 + - - +
71A ASP* 4.5 0.4 - - - -
72A LEU* 2.9 30.1 + - - +
418A TYR* 4.2 4.2 + - - +
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Residues in contact with CYS 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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47A LEU* 4.0 23.6 - - - -
65A LEU* 2.9 25.3 + - - -
66A SER 3.0 7.6 + - - +
68A ALA* 1.3 76.1 - - - +
70A ALA* 1.3 65.9 + - - +
72A LEU* 3.3 7.7 + - - +
73A ILE* 3.0 30.6 + - + +
150A TRP* 4.1 4.0 - - + -
502A Y01 3.7 40.4 - - + -
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Residues in contact with ALA 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 SER 3.0 8.6 + - - +
67A LEU* 3.6 8.1 - - - +
69A CYS* 1.3 75.5 - - - +
71A ASP* 1.3 63.1 + - - +
73A ILE* 3.1 5.7 + - - +
74A ILE* 3.0 28.8 + - + +
108A ALA* 3.5 26.4 - - - +
111A ALA* 4.6 0.4 - - + -
112A SER* 4.2 20.6 - - - +
115A ASN* 5.8 0.4 - - - +
150A TRP* 3.6 21.9 - - + -
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Residues in contact with ASP 71 (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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39A THR* 3.3 11.3 - - - +
43A ASN* 3.5 26.8 - - - +
67A LEU* 2.9 30.6 + - - +
68A ALA* 4.5 0.2 - - - -
70A ALA* 1.3 74.3 - - - +
72A LEU* 1.3 58.6 + - - +
74A ILE* 3.9 2.0 - - - +
75A GLY 2.9 22.2 + - - -
112A SER* 4.5 7.6 + - - -
410A ASN* 5.2 1.0 + - - -
411A SER* 2.9 37.0 + - - +
414A ASN* 3.0 35.5 + - - +
418A TYR* 5.7 0.3 + - - -
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Residues in contact with LEU 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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39A THR* 5.0 0.7 - - - -
40A VAL* 3.8 39.3 - - + +
43A ASN* 4.1 5.4 - - + +
44A LEU* 3.9 25.8 - - + +
47A LEU* 4.4 23.3 - - + -
68A ALA 2.9 21.8 + - - +
69A CYS* 3.5 7.0 - - - +
70A ALA 3.1 0.2 - - - -
71A ASP* 1.3 74.3 - - - +
73A ILE* 1.3 69.1 + - + +
75A GLY* 2.9 12.0 + - - -
76A THR* 2.9 24.3 + - + +
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Residues in contact with ILE 73 (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 CYS* 3.0 20.4 + - + +
70A ALA 3.5 6.3 - - - +
72A LEU* 1.3 76.2 - - + +
74A ILE* 1.3 65.2 + - - +
76A THR* 3.4 8.0 - - - +
77A PHE* 3.0 30.1 + - + -
78A SER* 3.7 5.1 + - - +
104A LEU* 3.7 39.7 - - + +
108A ALA* 3.7 16.8 - - + -
150A TRP* 3.8 28.7 - - + -
502A Y01 4.3 15.7 - - + -
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Residues in contact with ILE 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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70A ALA* 3.0 23.1 + - + +
71A ASP* 3.9 5.6 - - - +
73A ILE* 1.3 76.0 - - - +
75A GLY* 1.3 62.7 + - - +
78A SER* 3.1 23.6 + - - -
79A MET* 3.2 16.0 - - + +
105A ASP* 3.9 16.4 - - - +
108A ALA* 4.0 19.5 - - + +
109A SER* 3.8 22.9 - - - +
112A SER* 5.3 3.4 - - - -
378A TRP* 5.7 3.8 - - + -
408A TYR* 3.5 31.6 - - + -
411A SER* 3.7 28.9 - - - +
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Residues in contact with GLY 75 (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 SER* 2.8 26.9 + - - -
39A THR* 3.7 11.0 - - - -
40A VAL* 3.8 8.3 - - - +
71A ASP 2.9 13.2 + - - -
72A LEU 2.9 7.5 + - - -
74A ILE* 1.3 79.1 - - - +
76A THR* 1.3 59.0 + - - +
79A MET* 3.6 22.2 - - - +
80A ASN* 3.5 2.6 - - - +
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Residues in contact with THR 76 (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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40A VAL* 3.8 18.3 - - - +
72A LEU* 2.9 27.4 + - + +
73A ILE* 3.4 2.5 - - - +
75A GLY* 1.3 79.3 - - - +
77A PHE* 1.3 94.6 + - + +
80A ASN* 3.5 16.3 - - - +
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Residues in contact with PHE 77 (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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73A ILE* 3.0 19.8 + - + +
76A THR* 1.3 113.6 - - + +
78A SER* 1.3 69.8 + - - +
79A MET 3.6 1.1 - - - -
80A ASN* 3.4 3.6 + - - +
81A LEU* 3.0 46.4 + - + +
101A TRP* 5.5 1.3 - - + -
104A LEU* 3.8 31.4 - - + -
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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