Contacts of the helix formed by residues 62 - 74 (chain A) in PDB entry 5E6J
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 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PRO 3.7 0.2 - - - -
61A SER* 1.3 81.8 + - - +
63A ASP* 1.3 54.0 + - - +
64A THR* 2.7 28.4 + - - -
65A LEU* 2.9 24.8 + - - +
66A ARG* 2.8 47.5 + - - +
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Residues in contact with ASP 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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62A ASP* 1.3 75.4 - - - +
64A THR* 1.3 61.0 + - + +
66A ARG* 2.6 37.3 + - - +
67A SER* 2.8 33.0 + - - -
45C PHE* 5.9 0.7 - - - -
46C ALA* 4.0 24.3 - - + +
60C ASN* 5.1 10.6 - - - +
64F GLU* 6.0 3.1 - - - +
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Residues in contact with THR 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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18A HIS* 4.8 8.9 + - - -
62A ASP* 2.7 24.6 + - - -
63A ASP* 1.3 77.7 - - + +
65A LEU* 1.3 62.1 + - - +
67A SER* 3.2 5.7 + - - -
68A GLU* 2.8 44.8 + - - +
4F PHE* 3.7 31.4 - - + -
64F GLU* 4.4 17.0 - - - +
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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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10A THR* 5.0 7.6 - - - +
11A THR* 5.2 0.2 - - - -
12A VAL* 3.6 16.6 - - + +
18A HIS* 3.4 36.3 - - + +
58A VAL* 4.0 22.7 - - + -
60A PRO* 3.6 14.8 - - + +
61A SER* 3.9 23.1 - - - +
62A ASP* 2.9 22.5 + - - +
64A THR* 1.3 83.4 + - - +
66A ARG* 1.3 58.1 + - - +
68A GLU* 3.8 7.6 - - - +
69A ALA* 2.8 33.3 + - - +
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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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60A PRO* 3.5 23.8 + - + +
61A SER* 3.7 22.6 + - - +
62A ASP* 2.8 27.1 + - - +
63A ASP* 2.6 33.9 + - - +
65A LEU* 1.3 74.2 - - - +
67A SER* 1.3 57.1 + - - +
69A ALA* 3.8 0.9 - - - +
70A PHE* 2.9 32.6 + - - +
78A GLU* 3.5 25.0 + - + +
46C ALA 3.2 21.6 + - - +
47C GLY* 3.8 14.4 - - - +
48C LYS* 5.6 4.1 - - - +
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Residues in contact with SER 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 ASP 2.8 19.3 + - - -
64A THR* 3.5 6.1 - - - -
66A ARG* 1.3 77.1 - - - +
68A GLU* 1.3 58.6 + - - +
70A PHE* 3.3 3.9 + - - +
71A GLU* 2.9 36.4 + - - +
46C ALA* 3.9 15.3 + - - -
47C GLY 3.9 10.5 - - - +
68C HIS* 5.2 7.6 - - - -
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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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12A VAL* 3.7 12.9 + - + +
13A ASP* 3.5 17.3 - - - +
16A ASN* 3.5 30.3 - - - +
18A HIS* 3.0 39.9 + - - -
64A THR* 2.8 27.5 + - - +
65A LEU* 3.8 9.0 - - - +
67A SER* 1.3 75.1 + - - +
69A ALA* 1.3 52.8 + - - +
71A GLU* 3.0 8.8 + - - +
72A TYR* 2.7 36.5 + - - +
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Residues in contact with ALA 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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12A VAL* 3.4 21.7 - - + +
60A PRO* 4.2 20.0 - - + -
65A LEU 2.8 22.3 + - - +
66A ARG 3.8 3.1 - - - +
68A GLU* 1.3 72.7 - - - +
70A PHE* 1.3 57.7 + - - +
72A TYR* 3.2 4.8 + - - -
73A TYR* 2.8 45.9 + - + +
75A THR 5.1 1.1 - - - -
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Residues in contact with PHE 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 ARG 2.9 18.1 + - - +
67A SER* 3.6 4.7 - - - +
69A ALA* 1.3 78.1 - - - +
71A GLU* 1.3 63.7 + - - +
74A HIS* 2.6 49.7 + - - +
75A THR 3.3 29.8 - - - +
76A LEU* 3.9 13.0 - - + -
8C LEU* 4.1 22.7 - - + -
44C ILE* 3.5 38.6 - - + -
47C GLY* 4.0 14.4 - - - -
68C HIS* 3.7 39.3 - + + -
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Residues in contact with GLU 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 SER* 2.9 23.0 + - - +
68A GLU* 3.5 7.7 - - - +
70A PHE* 1.3 82.6 - - + +
72A TYR* 1.3 60.9 + - - +
74A HIS* 3.8 11.2 + - + -
131A PRO* 3.4 22.5 - - + +
6C LYS* 3.1 29.5 + - - -
66C THR* 5.5 1.2 + - - -
68C HIS* 3.4 24.1 + - - +
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Residues in contact with TYR 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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12A VAL 3.6 5.6 - - - -
13A ASP* 3.2 42.6 + - + -
14A ASN* 4.5 8.4 + - + +
15A THR* 4.9 3.1 - - - -
57A PHE* 5.5 2.4 - + - -
68A GLU 2.7 15.4 + - - +
69A ALA* 3.5 5.4 - - - +
71A GLU* 1.3 79.1 - - - +
73A TYR* 1.3 99.6 + + + +
84A TYR* 5.5 4.3 + + - -
130A ALA* 4.0 1.0 - - - +
131A PRO* 3.4 32.5 - - + +
132A ALA* 3.5 45.1 + - + +
135A GLU* 4.6 14.9 + - + -
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Residues in contact with TYR 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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12A VAL* 3.4 24.9 + - + -
57A PHE* 4.5 4.5 - - - -
69A ALA* 2.8 36.4 + - + +
72A TYR* 1.3 98.8 - + - +
74A HIS* 1.3 71.3 + - - +
75A THR* 3.2 20.6 + - + +
80A PHE* 3.4 35.7 - + + -
81A LEU* 3.5 30.7 - - + +
84A TYR* 3.7 21.9 - + - -
130A ALA* 4.0 1.7 - - - +
132A ALA* 4.2 5.2 - - + -
151A LEU* 4.2 3.1 - - + -
155A TYR* 2.9 34.5 + - - +
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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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70A PHE* 2.6 40.5 + + - -
71A GLU* 3.8 21.2 + - + -
73A TYR* 1.3 73.6 - - - +
75A THR* 1.3 56.0 + - - +
129A ASN* 2.7 46.4 + - + -
130A ALA* 3.6 7.4 - - + -
131A PRO* 4.1 3.3 - - + +
176A HIS* 3.3 29.6 - - - +
8C LEU* 3.4 51.8 + - + +
68C HIS* 5.8 3.1 - + - -
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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