Contacts of the helix formed by residues 61 - 74 (chain A) in PDB entry 1E0W
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 PHE 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A THR* 4.4 15.3 - - + -
59A PHE* 3.7 33.7 - + + -
60A ASN* 1.3 77.2 + - - +
62A SER* 1.3 59.3 + - - +
63A SER 3.5 2.2 - - - -
64A ALA* 4.0 5.4 - - + -
65A ASP* 2.8 37.2 + - - +
111A GLY 3.9 13.9 - - - -
112A VAL* 4.1 19.3 - - + -
115A HIS* 3.5 63.3 - + + +
116A TYR* 4.2 14.6 - + - +
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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
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60A ASN* 2.8 24.9 + - - -
61A PHE* 1.3 78.4 - - - +
63A SER* 1.3 67.3 + - - +
65A ASP* 4.0 3.3 - - - +
66A ARG* 3.2 41.0 + - - +
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Residues in contact with SER 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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22A SER* 4.3 9.3 - - - -
46A GLU* 3.5 29.8 + - - +
51A ALA* 4.8 7.6 + - - +
60A ASN* 4.8 1.1 + - - -
62A SER* 1.3 79.6 + - - +
64A ALA* 1.3 67.5 + - - +
66A ARG* 3.2 26.4 + - - +
67A VAL* 3.3 17.5 + - - +
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Residues in contact with ALA 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 GLU* 3.5 27.8 + - - +
47A MET* 3.8 19.5 - - + +
52A THR* 4.7 6.1 - - + -
60A ASN 5.3 0.6 + - - +
61A PHE* 3.4 13.1 + - + +
62A SER 3.4 0.4 - - - -
63A SER* 1.3 81.3 + - - +
65A ASP* 1.3 56.6 + - - +
67A VAL* 3.3 5.6 + - - +
68A TYR* 3.0 26.7 + - - +
116A TYR* 3.1 20.1 + - + +
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Residues in contact with ASP 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 PHE* 2.8 25.9 + - - +
62A SER* 4.1 3.8 - - - +
64A ALA* 1.3 70.8 - - - +
66A ARG* 1.3 59.3 + - - +
68A TYR* 4.2 7.5 - - - +
69A ASN* 2.8 47.5 + - - +
115A HIS* 2.9 31.4 + - - -
116A TYR* 2.7 31.6 + - - -
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Residues in contact with ARG 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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22A SER* 4.7 16.2 - - - -
25A LEU* 4.3 18.5 - - + +
62A SER* 3.2 31.8 + - - +
63A SER* 3.2 22.2 + - - +
65A ASP* 1.3 76.3 - - - +
67A VAL* 1.3 60.0 + - - +
69A ASN* 4.2 3.6 - - - +
70A TRP* 3.1 23.9 + - - +
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Residues in contact with VAL 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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20A ILE* 4.1 17.7 - - + +
22A SER* 4.0 18.6 - - - +
25A LEU* 5.0 3.1 - - + -
41A VAL* 4.0 22.9 - - + -
43A ALA* 4.0 23.6 - - + +
46A GLU* 3.9 26.9 - - + +
47A MET* 5.6 1.6 - - + -
63A SER 3.3 11.0 + - - +
64A ALA 3.3 7.6 + - - +
66A ARG* 1.3 75.0 - - - +
68A TYR* 1.3 66.4 + - - +
70A TRP* 3.3 6.9 + - + +
71A ALA* 3.0 21.8 + - - +
78A VAL* 6.2 1.6 - - + -
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Residues in contact with TYR 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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47A MET* 4.4 6.4 - - + +
64A ALA 3.0 16.7 + - - +
65A ASP* 3.9 7.4 - - - +
67A VAL* 1.3 77.2 - - - +
69A ASN* 1.3 78.0 + - - +
71A ALA* 3.2 7.6 + - - +
72A VAL* 3.0 52.1 + - + +
78A VAL* 4.0 23.6 - - + -
116A TYR* 4.1 27.4 - + + -
119A LYS* 3.5 59.4 + - + +
120A ILE* 4.6 3.6 - - + -
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Residues in contact with ASN 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 ASP* 2.8 37.2 + - - +
66A ARG* 4.2 3.9 - - - +
68A TYR* 1.3 86.1 - - - +
70A TRP* 1.3 67.1 + - - +
72A VAL* 3.5 8.8 - - - +
73A GLN* 3.0 48.5 + - - +
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Residues in contact with TRP 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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20A ILE* 4.0 29.4 - - + -
25A LEU* 4.0 33.4 - - + +
30A TYR* 6.4 0.2 - + - -
31A THR* 3.7 38.8 - - + +
34A ALA* 3.9 12.1 - - + -
35A GLY 3.9 17.5 - - - -
41A VAL* 4.2 5.4 - - + -
66A ARG 3.1 19.1 + - - +
67A VAL* 3.7 5.8 - - - +
69A ASN* 1.3 75.7 - - - +
71A ALA* 1.4 69.6 + - + +
73A GLN* 3.5 7.7 + - - +
74A ASN* 2.9 52.2 + - - +
76A LYS* 4.1 25.8 - - + -
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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
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41A VAL* 3.9 22.0 - - + -
67A VAL 3.0 12.7 + - - +
68A TYR 3.2 8.3 + - - +
70A TRP* 1.4 84.6 - - - +
72A VAL* 1.3 62.6 + - - +
74A ASN 3.2 9.2 + - - -
75A GLY 3.2 0.2 + - - -
76A LYS* 3.0 32.4 + - + +
78A VAL* 3.6 26.2 - - + -
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Residues in contact with VAL 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 TYR* 3.0 52.6 + - + +
69A ASN* 3.5 19.5 - - - +
71A ALA* 1.3 77.0 - - + +
73A GLN* 1.3 68.4 + - + +
75A GLY* 3.2 13.4 + - - -
76A LYS 4.0 13.7 - - - +
78A VAL* 4.9 1.8 - - + -
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Residues in contact with GLN 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 ASN* 3.0 42.4 + - - +
70A TRP* 3.9 8.4 - - - +
72A VAL* 1.3 79.6 - - + +
74A ASN* 1.3 65.5 + - - +
75A GLY 3.4 0.7 + - - -
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Residues in contact with ASN 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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31A THR 5.4 0.3 - - - +
35A GLY* 4.5 9.3 - - - +
70A TRP* 2.9 60.4 + - + +
71A ALA 3.2 2.2 + - - -
73A GLN* 1.3 83.4 + - - +
75A GLY* 1.3 56.0 + - - +
76A LYS* 2.9 38.7 + - + +
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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