Contacts of the helix formed by residues 60 - 79 (chain A) in PDB entry 4L2A
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 ASP 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A PHE* 5.8 1.2 - - - -
59A SER* 1.3 78.3 - - - +
61A GLY* 1.3 69.7 + - - +
62A GLY 3.6 0.2 + - - -
63A VAL* 3.4 8.0 + - - +
64A PHE* 3.1 18.4 + - - -
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Residues in contact with GLY 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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60A ASP* 1.3 78.4 - - - +
62A GLY* 1.3 55.0 + - - -
64A PHE* 3.0 4.6 + - - +
65A ASN* 2.8 43.8 + - - +
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Residues in contact with GLY 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.7 13.2 - - - +
60A ASP 3.6 0.2 + - - -
61A GLY* 1.3 70.9 - - - -
63A VAL* 1.3 62.9 + - - +
65A ASN* 4.5 7.2 - - - +
66A ASN* 3.0 33.2 + - - +
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.0 11.7 - - + +
41A LEU* 3.9 31.6 - - + +
42A ILE* 4.9 2.5 - - + -
47A PHE* 4.0 23.6 - - + -
55A ILE* 3.6 19.3 - - + -
59A SER* 3.6 19.3 - - - -
60A ASP 3.4 7.1 + - - +
61A GLY 3.2 0.6 - - - -
62A GLY* 1.3 76.3 - - - +
64A PHE* 1.3 65.4 + - - +
67A ALA* 3.0 23.6 + - - +
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Residues in contact with PHE 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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56A VAL* 3.3 28.7 - - - -
59A SER* 3.3 17.5 + - - +
60A ASP* 3.1 30.1 + - - +
61A GLY 3.0 4.1 + - - +
63A VAL* 1.3 79.5 - - - +
65A ASN* 1.3 76.7 + - - +
67A ALA* 4.8 1.3 - - - -
68A ALA* 2.9 48.5 + - + +
141A ALA* 3.8 26.5 - - + -
142A ALA* 4.0 13.0 - - + -
143A THR* 4.3 5.8 - - + -
146A THR* 4.1 16.4 - - + -
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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
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61A GLY* 2.8 28.0 + - - +
62A GLY* 4.0 6.7 - - - +
64A PHE* 1.3 85.7 - - - +
66A ASN* 1.3 60.4 + - - +
69A GLN* 3.1 35.5 + - - +
140A ASN* 5.6 0.7 - - - +
141A ALA* 3.6 10.6 + - - +
118B PHE* 3.3 53.2 - - + +
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Residues in contact with ASN 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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34A TYR* 3.3 41.0 - - - +
37A LYS* 3.2 42.7 - - - +
38A LEU* 4.1 13.0 - - + +
41A LEU* 4.0 6.7 - - + +
62A GLY* 3.0 29.2 + - - +
63A VAL 4.3 0.7 - - - +
65A ASN* 1.3 77.0 - - - +
67A ALA* 1.3 66.2 + - - +
69A GLN 3.4 0.5 + - - -
70A ILE* 3.0 29.3 + - - +
118B PHE* 5.7 2.5 - - - -
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Residues in contact with ALA 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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38A LEU* 4.1 7.0 - - + +
52A LEU* 3.5 20.1 - - + +
55A ILE* 3.5 26.7 - - + -
56A VAL* 3.5 17.6 - - + +
63A VAL 3.0 19.7 + - - +
64A PHE 4.0 0.9 - - - +
66A ASN* 1.3 75.4 - - - +
68A ALA* 1.3 58.6 - - - +
70A ILE* 3.0 11.3 + - - +
71A TRP 2.9 23.4 + - - -
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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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56A VAL* 3.4 13.1 - - + +
64A PHE* 2.9 38.5 + - + +
67A ALA* 1.3 75.6 - - - +
69A GLN* 1.3 52.8 + - - +
71A TRP* 2.9 3.9 + - - +
72A ASN* 2.7 40.4 + - - -
141A ALA* 3.3 27.1 - - + +
143A THR* 4.2 7.2 - - + -
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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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34A TYR* 3.1 53.3 + - + -
65A ASN 3.1 26.0 + - - +
66A ASN 3.8 0.4 - - - +
67A ALA 3.2 0.2 - - - -
68A ALA* 1.3 77.3 - - - +
70A ILE* 1.3 64.3 + - - +
72A ASN* 3.0 28.0 + - - +
73A HIS* 2.8 47.3 + - - -
122A TRP* 3.3 12.4 + - - -
141A ALA* 3.5 14.8 - - + -
159A TRP* 3.3 28.6 - - - +
118B PHE* 3.8 4.3 - - + -
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Residues in contact with ILE 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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2A PHE* 5.2 6.3 - - + -
3A GLU 5.5 1.8 - - - +
5A PRO* 5.4 4.5 - - + -
31A HIS* 3.2 18.6 + - + +
34A TYR* 3.7 29.2 - - + +
35A VAL* 3.7 27.6 - - + -
38A LEU* 3.8 28.5 - - + -
52A LEU* 3.7 19.7 - - + -
66A ASN 3.0 22.1 + - - +
67A ALA* 3.4 5.6 - - - +
69A GLN* 1.3 77.1 - - - +
71A TRP* 1.3 64.6 + - - +
74A THR* 3.1 25.7 + - - +
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Residues in contact with TRP 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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52A LEU* 4.0 20.1 - - + +
53A GLU* 3.2 39.5 + - + +
56A VAL* 4.3 5.2 - - + -
67A ALA 2.9 12.4 + - - +
68A ALA* 2.9 10.7 + - - +
70A ILE* 1.3 78.3 - - - +
72A ASN* 1.3 76.4 + - - +
74A THR* 3.2 6.7 + - + -
75A PHE* 3.0 52.2 + + + +
124A TRP* 3.8 18.8 - + - -
143A THR* 3.6 19.1 - - + -
145A LEU* 3.8 26.9 - - + -
152A PRO* 3.7 22.9 - - + -
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Residues in contact with ASN 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 ALA 2.7 20.0 + - - +
69A GLN* 3.0 22.8 + - - +
71A TRP* 1.3 79.6 - - - +
73A HIS* 1.3 59.8 + - - +
75A PHE* 3.4 4.1 + - - +
76A TYR* 2.8 28.9 + - - +
122A TRP* 3.4 32.7 - - + +
124A TRP* 3.4 14.9 - - + -
141A ALA 3.1 23.4 + - - -
142A ALA 4.0 2.0 + - - -
143A THR* 3.1 26.3 + - - +
155A THR* 4.1 1.4 - - - +
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Residues in contact with HIS 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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26A HIS* 3.1 22.4 + + - -
30A HIS* 5.0 0.6 - - - +
31A HIS* 3.6 27.8 - + + +
34A TYR* 3.5 19.9 - + - -
69A GLN* 2.8 57.6 + - - +
72A ASN* 1.3 73.8 - - - +
74A THR* 1.3 69.7 + - - +
76A TYR* 3.1 6.8 + + - +
77A TRP* 2.9 35.3 + + - +
122A TRP* 3.7 9.7 - + - -
157A ASP* 3.4 3.8 + - - -
161A HIS* 3.6 2.0 + - - -
5000A FE 2.0 31.1 - - - -
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Residues in contact with THR 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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5A PRO* 3.6 22.9 - - + +
31A HIS* 3.3 18.1 + - - -
52A LEU* 5.7 1.4 - - - +
70A ILE* 3.1 18.5 + - - +
71A TRP* 3.5 11.0 - - + -
73A HIS* 1.3 79.2 - - - +
75A PHE* 1.3 61.9 + - - +
77A TRP* 3.3 7.9 + - - +
78A ASN* 3.2 31.9 + - - +
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Residues in contact with PHE 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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71A TRP* 3.0 53.0 + + + +
72A ASN* 3.5 5.4 - - - +
74A THR* 1.3 78.5 - - - +
76A TYR* 1.3 57.6 + - - +
78A ASN* 3.3 2.9 + - - -
79A SER* 2.8 31.9 + - - -
124A TRP* 3.7 20.2 - + - -
152A PRO* 3.4 34.3 - - + -
153A ILE 3.5 8.5 - - - -
154A LEU* 3.5 29.6 - - - -
155A THR* 3.8 7.9 - - + -
186A PHE* 3.6 25.6 - + - -
190A ASN* 3.6 10.3 - - - -
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Residues in contact with TYR 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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18A ILE* 3.8 16.5 - - - +
26A HIS* 3.6 19.2 + + - -
72A ASN 2.8 17.8 + - - +
73A HIS* 3.1 7.6 + + - +
75A PHE* 1.3 73.8 - - - +
77A TRP* 1.3 102.4 + + - +
79A SER* 2.9 16.1 + - - -
80A LEU* 3.5 27.1 - - + +
122A TRP* 3.8 5.4 - - + -
155A THR* 3.5 28.2 - - + +
156A VAL* 4.2 5.8 - - + -
157A ASP* 3.5 30.5 - - + -
162A ALA* 4.3 5.7 + - - +
174A TYR* 2.7 26.0 + - - -
178A PHE* 5.3 0.4 - + - -
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Residues in contact with TRP 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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5A PRO* 5.8 2.0 - - + -
6A SER 5.9 0.9 - - - -
7A LEU* 3.6 20.4 - - + -
8A PRO* 3.9 17.0 - - + -
9A TYR* 2.7 45.8 + - - +
18A ILE* 6.1 0.2 - - + -
23A LEU* 3.8 22.4 - - + -
26A HIS* 3.3 42.4 - + + -
27A HIS* 3.5 32.3 + + + -
31A HIS* 2.8 34.4 + + - -
73A HIS* 2.9 27.5 + + + -
74A THR* 3.8 6.5 - - - +
76A TYR* 1.3 97.7 - + - +
78A ASN* 1.3 63.1 + - - +
80A LEU* 3.3 8.5 + - + +
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Residues in contact with ASN 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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8A PRO* 3.7 23.8 - - - +
74A THR* 3.2 25.3 + - - +
75A PHE* 3.7 3.0 - - - +
76A TYR 3.1 1.0 - - - -
77A TRP* 1.3 80.4 - - - +
79A SER* 1.3 55.6 + - - +
80A LEU 3.1 2.7 - - - -
183A ASN* 3.0 29.6 + - - +
186A PHE* 3.2 43.3 - - + +
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Residues in contact with SER 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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75A PHE* 2.8 17.4 + - - -
76A TYR 2.9 12.2 + - - -
78A ASN* 1.3 76.0 - - - +
80A LEU* 1.3 57.7 + - - +
154A LEU* 3.6 16.0 - - - +
155A THR 3.2 39.0 + - - -
178A PHE* 4.2 3.5 - - - -
182A VAL* 3.5 10.6 - - - +
183A ASN* 2.8 27.8 + - - -
186A PHE* 3.8 10.8 - - - -
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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