Contacts of the helix formed by residues 61 - 76 (chain A) in PDB entry 1E5E
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 ASN 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 2.9 35.1 + - - +
32A THR 3.8 2.4 + - - -
35A PHE* 3.8 6.0 - - - -
54A TYR* 3.3 7.4 - - - -
57A THR* 3.1 30.5 + - + +
60A GLY* 1.3 75.7 - - - +
62A PRO* 1.3 67.0 - - - +
63A THR* 3.0 33.6 + - - -
64A VAL* 3.1 18.3 + - + +
65A SER* 2.8 29.2 + - - -
247A PRO* 3.6 11.9 - - - +
411A GOL 4.6 2.2 + - - +
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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
----------------------------------------------------------
18A GLN* 4.2 8.9 - - - +
30A TYR* 3.8 35.4 - - + -
35A PHE* 3.5 20.9 - - + -
54A TYR* 3.6 34.7 - - + +
61A ASN* 1.3 93.0 - - - +
63A THR* 1.3 59.9 + - - +
65A SER* 3.8 1.4 - - - -
66A ASN* 3.0 22.5 + - - +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PRO 3.1 13.1 + - - -
29A ILE* 4.8 0.7 - - - -
30A TYR* 2.8 30.5 + - - +
61A ASN* 3.0 10.0 + - - -
62A PRO* 1.3 78.6 - - - +
64A VAL* 1.3 63.9 + - - +
66A ASN* 3.3 15.1 + - - +
67A LEU* 3.4 11.6 + - - +
247A PRO* 3.3 28.7 - - - +
250A ALA* 4.1 2.9 - - + +
251A TRP* 3.7 28.9 - - + +
254A THR* 5.0 1.6 + - - +
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Residues in contact with VAL 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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57A THR* 5.7 0.4 - - + -
61A ASN* 3.1 27.2 + - + +
63A THR* 1.3 74.9 - - - +
65A SER* 1.3 64.9 + - - +
67A LEU* 3.3 5.6 + - + +
68A GLU* 3.0 47.3 + - - +
82A ALA* 3.9 8.5 - - + -
233A ARG* 5.7 0.2 - - - +
245A ILE* 3.5 42.0 - - + +
247A PRO* 4.3 8.3 - - + -
250A ALA* 3.9 15.3 - - + -
411A GOL 3.9 15.0 - - - +
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 3.4 5.1 + - - -
18A GLN* 5.5 0.7 - - - -
54A TYR* 2.8 31.7 + - - -
60A GLY* 5.6 0.5 - - - -
61A ASN 2.8 12.3 + - - -
62A PRO* 3.8 3.6 - - - -
64A VAL* 1.3 71.8 - - - +
66A ASN* 1.3 67.5 + - - +
68A GLU* 3.2 16.3 + - - +
69A GLY* 3.0 20.6 + - - -
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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
----------------------------------------------------------
16A ASN* 3.1 26.5 + - - +
18A GLN* 3.4 29.5 + - - +
27A PRO* 4.1 18.1 - - + +
62A PRO 3.0 12.8 + - - +
63A THR* 3.5 12.8 - - - +
64A VAL 3.2 0.6 - - - -
65A SER* 1.3 76.7 - - - +
67A LEU* 1.3 62.7 + - - +
70A LYS* 2.6 44.4 + - - +
254A THR* 4.0 18.2 + - - +
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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
----------------------------------------------------------
63A THR 3.4 6.7 + - - +
64A VAL 3.3 9.0 + - - +
66A ASN* 1.3 78.6 - - - +
68A GLU* 1.3 63.8 + - - +
70A LYS* 3.2 5.3 + - - +
71A ILE* 3.0 41.2 + - + +
82A ALA* 4.4 11.0 - - + -
221A LEU* 4.1 16.4 - - + -
245A ILE* 4.6 0.4 - - + -
250A ALA* 4.1 15.7 - - + +
253A ILE* 3.8 48.7 - - + -
254A THR* 3.5 27.5 + - - +
257A LEU* 4.5 7.4 - - + -
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Residues in contact with GLU 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 VAL* 3.0 31.7 + - - +
65A SER* 3.2 21.0 + - - +
67A LEU* 1.3 75.7 - - + +
69A GLY* 1.3 55.6 + - - +
71A ILE 3.3 1.0 + - - -
72A ALA* 2.8 27.6 + - - +
80A CYS* 3.2 45.5 - - - +
81A VAL* 3.3 0.3 - - - -
82A ALA* 2.8 37.1 + - + +
233A ARG* 3.2 28.5 + - - -
411A GOL 4.3 2.1 - - - -
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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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16A ASN* 3.4 26.2 - - - +
65A SER 3.0 11.3 + - - -
68A GLU* 1.3 72.5 - - - +
70A LYS* 1.3 65.5 + - - +
72A ALA* 3.9 6.9 - - - +
73A PHE* 3.0 25.3 + - - +
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Residues in contact with LYS 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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11A ALA 4.9 2.7 - - - +
12A CYS 4.7 4.7 - - - +
13A ILE 3.7 21.7 + - - -
14A HIS 5.2 0.4 - - - -
15A ALA* 3.0 36.3 + - + +
16A ASN* 3.2 10.6 + - + +
17A PRO* 4.6 3.0 - - - +
18A GLN* 4.7 2.0 - - - +
27A PRO* 6.0 0.4 - - - +
66A ASN* 2.6 42.4 + - - +
67A LEU 3.2 7.4 + - - +
69A GLY* 1.3 78.0 - - - +
71A ILE* 1.3 56.5 + - - +
73A PHE* 3.3 3.5 + - - +
74A LEU* 3.0 32.9 + - + +
254A THR* 4.0 26.7 - - + +
257A LEU* 4.0 20.9 - - + -
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Residues in contact with ILE 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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67A LEU* 3.0 28.7 + - + +
68A GLU 3.8 3.1 - - - +
70A LYS* 1.3 71.3 - - - +
72A ALA* 1.3 61.7 + - - +
74A LEU* 3.1 8.1 + - + +
75A GLU* 2.9 34.0 + - + +
80A CYS* 3.9 8.3 - - - -
190A PRO* 5.0 6.1 - - + -
205A HIS* 5.1 2.0 - - + -
211A ILE* 3.9 31.2 - - + -
221A LEU* 3.9 24.7 - - + -
223A CYS* 3.6 26.7 - - - -
257A LEU* 4.0 21.8 - - + -
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Residues in contact with ALA 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 GLU 2.8 21.5 + - - +
69A GLY* 3.9 7.4 - - - +
71A ILE* 1.3 73.5 - - - +
73A PHE* 1.3 63.7 + - - +
76A LYS* 3.0 4.3 + - - -
77A THR* 2.9 55.5 + - - +
78A GLU 4.3 2.7 - - - +
79A ALA* 3.8 20.0 - - - +
80A CYS* 3.9 3.8 - - - +
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Residues in contact with PHE 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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5A ARG* 3.0 70.9 + - + +
6A MET* 3.9 24.7 - - + -
7A THR 5.6 0.2 - - - -
8A PRO* 6.1 0.2 - - + -
11A ALA* 3.7 31.6 - - + -
15A ALA* 3.8 16.6 - - + -
16A ASN* 5.5 2.0 - - + +
69A GLY 3.0 19.3 + - - +
70A LYS 3.5 4.7 - - - +
72A ALA* 1.3 77.2 - - - +
74A LEU* 1.3 65.8 + - + +
76A LYS* 3.2 8.3 + - - +
77A THR 5.3 0.2 - - - -
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Residues in contact with LEU 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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8A PRO* 4.1 11.0 - - + +
11A ALA* 3.8 30.1 - - + +
12A CYS* 4.1 15.5 - - + +
15A ALA* 5.6 0.2 - - + -
70A LYS 3.0 19.6 + - - +
71A ILE* 3.1 10.9 + - + +
73A PHE* 1.3 78.2 - - + +
75A GLU* 1.3 56.3 + - - +
76A LYS* 3.7 1.2 + - - +
190A PRO* 3.7 21.6 - - + +
191A MET* 3.7 23.3 - - + -
194A ASN* 3.0 23.4 + - - +
257A LEU* 3.7 36.3 - - + -
260A LEU* 4.9 0.4 - - + -
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Residues in contact with GLU 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 ILE* 2.9 17.8 + - + +
72A ALA 4.3 0.9 - - - +
74A LEU* 1.3 74.2 - - - +
76A LYS* 1.3 69.3 + - - +
77A THR* 3.4 18.4 + - + +
185A ASN* 2.8 17.0 + - - -
190A PRO* 3.5 22.1 - - + +
193A THR 3.5 0.3 - - - +
194A ASN* 3.1 29.4 + - - +
195A PRO* 3.5 4.5 - - - +
196A VAL* 3.5 16.8 - - - +
203A VAL* 3.7 9.7 - - + +
205A HIS* 2.7 27.7 + - - +
223A CYS* 4.0 19.1 - - + -
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Residues in contact with LYS 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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5A ARG* 3.6 46.1 - - - +
72A ALA 3.0 6.4 + - - -
73A PHE 3.2 7.2 + - - +
74A LEU 4.6 1.1 - - - +
75A GLU* 1.3 80.7 - - - +
77A THR* 1.3 58.9 + - - +
194A ASN* 3.8 19.3 + - - +
196A VAL* 3.9 15.7 - - + +
197A ASP* 4.1 22.8 + - - +
306A ARG* 4.8 6.5 - - - +
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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