Contacts of the helix formed by residues 60 - 80 (chain A) in PDB entry 4BR6
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 LEU 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 4.3 10.6 - - + +
44A ALA* 3.5 50.7 - - + +
45A THR* 3.5 17.7 - - - +
56A LYS* 3.3 35.2 - - - +
57A ALA 3.3 8.2 + - - +
58A ALA 3.0 1.2 - - - -
59A SER* 1.3 82.0 - - - +
61A ALA* 1.3 63.2 + - - +
62A PRO 3.4 1.6 - - - -
63A LEU* 3.2 28.5 + - + +
64A LEU* 3.1 21.5 + - + +
64C LEU* 5.2 0.9 - - - -
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Residues in contact with ALA 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 ALA 4.0 1.6 + - - -
58A ALA 3.0 17.7 + - - +
60A LEU* 1.3 77.7 - - - +
62A PRO* 1.3 68.2 - - + +
64A LEU* 3.3 6.6 + - - -
65A ASN* 3.1 19.9 + - - +
61C ALA* 3.6 16.2 - - - +
64C LEU* 3.9 13.9 - - + -
65C ASN* 3.7 33.0 - - + +
601C NA 3.8 2.1 - - - -
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Residues in contact with PRO 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA 4.0 1.8 - - - +
59A SER* 3.6 17.0 - - - +
60A LEU 3.6 0.2 - - - -
61A ALA* 1.3 95.7 - - + +
63A LEU* 1.3 57.5 + - + +
65A ASN* 3.5 4.4 + - + +
66A PHE* 3.1 29.0 + - - +
122B GLN* 4.1 16.1 - - - +
65C ASN* 4.2 8.7 - - - +
601C NA 3.6 16.2 - - - -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY 5.3 0.2 - - - +
41A ALA* 4.4 11.9 - - + -
59A SER 5.5 2.2 - - - +
60A LEU* 3.2 30.7 + - + +
62A PRO* 1.3 76.7 - - + +
64A LEU* 1.3 61.2 + - - +
66A PHE* 4.4 2.2 - - - -
67A HIS* 2.8 61.1 + - + +
122B GLN* 3.6 21.1 - - - +
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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
----------------------------------------------------------
38A LEU* 3.6 26.7 - - + -
41A ALA* 4.2 12.3 - - + +
42A LEU* 3.7 24.2 - - + -
45A THR* 5.6 6.1 - - + +
60A LEU 3.1 13.6 + - - +
61A ALA* 3.6 8.5 - - - +
63A LEU* 1.3 78.2 - - - +
65A ASN* 1.3 57.0 + - - +
67A HIS* 5.2 0.2 - - - -
68A GLY* 2.8 31.3 + - - +
45C THR* 4.7 9.4 - - + +
57C ALA 3.6 19.7 - - - +
58C ALA* 4.1 11.2 - - - +
60C LEU 5.1 0.4 - - - -
61C ALA* 4.1 17.9 - - + +
64C LEU* 4.7 15.3 - - + -
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Residues in contact with ASN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA 3.1 16.2 + - - +
62A PRO 3.7 5.0 + - - +
64A LEU* 1.3 77.4 - - - +
66A PHE* 1.3 59.7 + - - +
69A GLY* 2.8 30.5 + - - +
146A GLN 4.2 2.3 - - - +
147A ASP* 2.8 30.3 + - - +
148A PRO* 3.9 17.8 - - - +
58C ALA* 4.5 5.5 - - - +
61C ALA* 3.6 14.4 - - + +
62C PRO* 4.4 17.9 - - - +
601C NA 4.6 6.1 - - - -
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Residues in contact with PHE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.6 27.6 - + - -
62A PRO 3.1 15.8 + - - +
63A LEU* 3.9 2.2 - - + +
65A ASN* 1.3 83.9 - - - +
67A HIS* 1.3 81.3 + + - +
70A GLY* 3.0 22.2 + - - -
145A ASN* 4.9 3.8 - - + -
146A GLN* 3.3 40.0 - - + +
162A TRP* 4.0 16.6 - + - -
121B ILE 5.5 0.7 - - - -
122B GLN* 3.7 56.1 - - + +
123B GLY 4.3 0.7 - - - -
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Residues in contact with HIS 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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33A THR* 3.9 21.5 - - + -
34A TYR* 3.5 32.6 - + - +
37A GLY* 3.5 25.0 - - - -
38A LEU* 3.3 20.4 - - - +
63A LEU* 2.8 53.2 + - + +
66A PHE* 1.3 91.0 - + - +
68A GLY* 1.3 60.4 + - - +
70A GLY* 3.2 1.9 + - - -
71A HIS* 2.9 29.3 + - - +
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Residues in contact with GLY 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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38A LEU* 3.8 22.4 - - - +
64A LEU 2.8 21.9 + - - -
67A HIS* 1.3 73.3 - - - +
69A GLY* 1.3 60.6 + - - +
71A HIS* 3.5 2.9 + - - +
72A LEU* 3.2 22.9 + - - +
54C PHE 5.2 1.4 - - - +
55C THR* 6.0 0.2 - - - -
58C ALA* 3.7 22.3 - - - +
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Residues in contact with GLY 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 ASN 2.8 26.1 + - - -
68A GLY* 1.3 71.4 - - - +
70A GLY* 1.3 57.8 + - - +
72A LEU* 3.2 2.9 + - - +
73A ASN* 2.9 40.8 + - - +
146A GLN 3.2 13.2 - - - -
148A PRO* 4.2 16.6 - - - -
58C ALA* 4.3 1.2 - - - +
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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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31A HIS* 4.3 0.2 - - - -
34A TYR* 3.9 12.1 - - - -
66A PHE 3.0 16.0 + - - -
67A HIS 3.2 3.1 + - - -
69A GLY* 1.3 76.6 - - - +
71A HIS* 1.3 61.0 + - - +
74A HIS* 2.5 34.2 + - - +
146A GLN* 3.5 25.8 - - - +
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Residues in contact with HIS 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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2A ALA* 4.1 12.0 - - + +
3A THR 3.4 27.5 + - - -
5A PRO* 4.3 3.4 - - + -
31A HIS* 3.1 26.1 + - + -
34A TYR* 3.8 8.4 - - + +
35A VAL* 3.8 11.2 - - + +
38A LEU* 3.9 27.1 - - + -
67A HIS 2.9 15.9 + - - +
68A GLY 3.8 5.2 - - - +
69A GLY 3.3 0.2 - - - -
70A GLY* 1.3 75.7 - - - +
72A LEU* 1.3 59.3 + - + +
75A THR* 2.5 48.9 + - - -
54C PHE* 4.4 15.1 - - + +
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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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68A GLY 3.2 14.8 + - - +
69A GLY 3.2 3.7 + - - +
71A HIS* 1.3 80.8 - - + +
73A ASN* 1.3 68.2 + - - +
75A THR* 3.3 7.0 + - + -
76A LEU* 3.1 54.0 + - + +
148A PRO* 3.7 27.4 - - + -
149A VAL 4.6 7.0 - - - +
150A THR* 4.4 8.7 - - + -
155A PRO* 5.8 1.1 - - + -
55C THR* 3.3 45.8 - - + +
58C ALA* 6.2 1.8 - - + -
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Residues in contact with ASN 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 GLY 2.9 20.7 + - - +
70A GLY 4.2 0.7 - - - +
72A LEU* 1.3 79.1 - - - +
74A HIS* 1.3 58.0 - - - +
76A LEU* 3.6 2.8 + - - +
77A PHE* 3.0 26.9 + - - +
126A TRP* 3.5 32.9 - - + +
128A TRP* 3.8 22.5 - - + -
146A GLN* 2.8 47.8 + - - +
147A ASP 4.1 3.5 + - - -
148A PRO* 3.7 20.9 - - - +
149A VAL 4.6 0.9 + - - -
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Residues in contact with HIS 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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26A HIS* 3.6 18.9 - + - -
31A HIS* 3.6 24.2 - + + +
34A TYR* 3.3 31.8 - + - -
70A GLY* 2.5 26.2 + - - +
73A ASN* 1.3 73.5 - - - +
75A THR* 1.3 65.9 + - - +
77A PHE* 3.4 5.4 - + - +
78A TRP* 2.9 41.6 + + + -
126A TRP* 3.7 13.3 - + - -
146A GLN* 3.5 19.7 - - - -
301A MN3 2.3 35.4 + - - -
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Residues in contact with THR 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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5A PRO* 4.0 15.4 - - + +
31A HIS* 3.6 14.5 + - - -
71A HIS* 2.5 37.2 + - + -
72A LEU* 3.3 8.4 + - + -
74A HIS* 1.3 78.3 - - - +
76A LEU* 1.3 69.6 + - + +
78A TRP* 3.5 7.2 + - - -
79A GLU* 3.3 38.8 + - - +
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Residues in contact with LEU 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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72A LEU* 3.1 38.5 + - + +
73A ASN 3.9 3.8 - - - +
75A THR* 1.3 83.4 - - + +
77A PHE* 1.3 67.5 + - - +
79A GLU* 3.1 9.2 + - - +
80A ASN* 2.9 22.9 + - - +
128A TRP* 3.9 22.2 - - + -
155A PRO* 3.6 33.4 - - + +
193A ARG* 3.0 35.3 + - - +
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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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18A ILE* 5.1 3.8 - - + -
23A MET* 6.1 0.9 - - - -
26A HIS* 4.1 22.9 - + - -
73A ASN 3.0 19.9 + - - +
74A HIS* 3.2 7.2 + + - +
76A LEU* 1.3 76.8 - - - +
78A TRP* 1.3 84.5 + + - +
80A ASN* 3.2 25.8 + - - -
81A LEU* 3.4 30.7 + - + +
126A TRP* 3.6 21.1 - + + -
128A TRP* 5.0 0.9 - - - -
158A GLY 3.2 25.6 - - - -
159A ILE* 3.8 3.1 - - + -
160A ASP* 3.7 15.3 - - + -
165A ALA* 5.5 0.2 - - + -
177A TYR* 3.8 10.3 - - - -
181A ILE* 3.8 26.7 - - + -
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Residues in contact with TRP 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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5A PRO* 4.5 10.1 - - + -
6A ASP 6.0 0.4 - - - -
7A LEU* 3.4 28.0 - - + -
8A LYS* 4.7 6.3 + - - +
9A TYR* 4.8 4.6 - - + -
23A MET* 4.1 28.7 - - + -
26A HIS* 3.6 59.0 - + + -
27A HIS* 4.0 16.5 - + + -
31A HIS* 3.0 32.9 + + + -
74A HIS* 2.9 30.7 + + + -
75A THR* 4.0 9.0 - - - +
77A PHE* 1.3 91.5 - + - +
79A GLU* 1.3 57.9 + - + +
81A LEU* 3.0 33.3 + - + +
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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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8A LYS* 4.0 25.8 + - - +
75A THR* 3.3 28.3 + - + +
76A LEU* 3.1 11.7 + - - +
78A TRP* 1.3 79.1 - - + +
80A ASN* 1.3 56.5 + - - +
81A LEU 3.4 3.6 + - - +
186A ASN* 3.8 7.1 + - - -
189A THR* 3.0 29.6 + - + +
193A ARG* 2.9 28.3 + - - +
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Residues in contact with ASN 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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76A LEU 2.9 19.5 + - - +
77A PHE* 3.2 11.9 + - - -
79A GLU* 1.3 74.3 - - - +
81A LEU* 1.3 61.2 + - - +
128A TRP* 4.7 0.3 - - - -
157A MET* 4.1 10.4 - - + +
158A GLY* 3.1 43.7 + - - +
159A ILE* 5.6 0.2 - - - +
185A ILE* 3.4 8.8 - - - +
186A ASN* 3.1 33.7 + - - +
189A THR* 4.5 1.3 - - + -
190A VAL* 4.1 9.6 - - + -
193A ARG* 3.3 24.6 + - - +
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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
------------------------------------------------------------
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