Contacts of the helix formed by residues 61 - 74 (chain A) in PDB entry 2ABQ
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 GLY 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLY* 1.3 73.8 - - - +
62A PHE* 1.3 60.3 + - - -
63A THR 3.2 0.2 - - - -
65A ALA* 3.0 26.4 + - - +
68A ARG* 5.8 0.2 + - - -
82A GLU* 3.6 10.0 + - - +
83A VAL 4.5 1.0 + - - -
84A GLU 4.9 2.5 + - - -
85A GLY 3.7 3.4 + - - -
86A ASP* 3.1 18.2 - - - -
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Residues in contact with PHE 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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61A GLY* 1.3 72.1 - - - -
63A THR* 1.3 89.5 + - + +
65A ALA* 3.3 9.2 + - - +
66A TYR* 3.0 21.3 + - - +
86A ASP* 4.2 9.4 + - - -
89A ILE* 4.6 3.6 - - + -
11B ILE* 4.1 24.7 - - + -
33B LYS* 3.7 28.9 - - + -
62B PHE* 4.1 27.5 - + - +
63B THR* 5.4 0.4 - - + -
66B TYR* 3.8 44.9 - + + -
89B ILE* 6.3 1.1 - - + -
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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
----------------------------------------------------------
11A ILE* 3.6 26.6 - - + +
60A GLY 3.5 1.0 + - - -
62A PHE* 1.3 114.5 - - + +
64A GLY* 1.3 62.2 + - - +
66A TYR* 3.2 5.2 + - - +
67A VAL* 3.1 24.6 + - - +
86A ASP* 3.8 4.0 - - - +
87A THR* 2.6 42.1 + - - +
89A ILE* 3.9 19.5 - - + -
33B LYS* 4.2 2.2 - - - +
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.7 16.8 - - - +
60A GLY 2.9 23.3 + - - -
61A GLY 3.1 0.9 + - - -
63A THR* 1.3 75.2 + - - +
65A ALA* 1.3 60.1 - - - +
67A VAL* 3.1 5.2 + - - +
68A ARG* 2.9 32.8 + - - +
87A THR* 3.5 15.5 - - - -
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Residues in contact with ALA 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 3.0 12.5 + - - +
62A PHE* 3.5 13.7 - - - +
63A THR 3.2 0.2 - - - -
64A GLY* 1.3 77.0 - - - +
66A TYR* 1.3 56.6 + - - +
68A ARG* 3.7 16.2 - - - +
69A ASN* 2.8 32.1 + - - +
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Residues in contact with TYR 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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11A ILE* 3.5 30.5 - - + -
33A LYS* 2.9 35.8 + - + +
34A GLN* 3.6 6.0 - - - -
35A PRO* 3.9 26.4 - - + +
62A PHE 3.0 12.7 + - - +
63A THR 3.3 8.1 - - - +
65A ALA* 1.3 77.2 - - - +
67A VAL* 1.3 66.4 + - - +
69A ASN* 3.7 9.6 + - - +
70A ALA* 3.0 27.8 + - + +
62B PHE* 3.4 50.0 - + + -
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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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10A SER 3.8 23.3 - - - +
11A ILE* 4.2 10.8 - - + -
35A PRO* 4.0 15.2 - - + +
40A ILE* 3.9 28.9 - - + -
59A LEU* 4.0 17.0 - - + -
63A THR 3.1 15.2 + - - +
64A GLY* 3.1 9.7 + - - +
66A TYR* 1.3 81.9 - - + +
68A ARG* 1.3 62.3 + - - +
70A ALA* 3.4 2.6 + - - +
71A LEU* 3.2 29.4 + - + +
87A THR* 4.6 7.6 - - + -
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Residues in contact with ARG 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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59A LEU* 4.0 31.3 - - + +
61A GLY 5.8 0.2 + - - -
64A GLY 2.9 17.3 + - - +
65A ALA* 3.7 20.3 - - - +
67A VAL* 1.3 75.2 - - - +
69A ASN* 1.3 67.1 + - - +
71A LEU* 3.4 1.7 + - - -
72A GLU* 3.0 35.3 + - - +
78A LEU* 3.8 24.2 - - + +
80A PHE* 4.1 22.4 + - + +
82A GLU* 3.4 33.9 + - - +
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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 ALA 2.8 18.7 + - - +
66A TYR* 3.7 12.1 + - - +
68A ARG* 1.3 77.4 - - - +
70A ALA* 1.3 64.9 + - - +
72A GLU* 3.0 19.8 - - - +
73A LYS* 2.8 65.9 + - - +
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Residues in contact with ALA 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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35A PRO* 3.8 28.3 - - + -
66A TYR* 3.0 23.7 + - + +
67A VAL 3.5 5.2 - - - +
69A ASN* 1.3 80.2 - - - +
71A LEU* 1.3 64.0 + - - +
73A LYS* 2.8 21.8 + - - +
74A GLU* 2.9 18.2 + - - +
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Residues in contact with LEU 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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35A PRO* 4.5 6.1 - - + -
40A ILE* 4.2 25.6 - - + +
43A SER* 5.7 0.9 - - - -
44A ARG* 4.2 9.2 - - + -
55A ALA* 4.6 9.0 - - + -
67A VAL* 3.2 24.3 + - + +
68A ARG 4.0 2.7 - - - +
70A ALA* 1.3 78.5 - - - +
72A GLU* 1.3 62.1 + - - +
74A GLU* 3.1 18.7 + - - +
76A ILE* 3.1 50.5 + - + +
78A LEU* 4.0 11.2 - - + -
80A PHE* 3.5 38.1 - - + -
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Residues in contact with GLU 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 ARG* 3.0 29.7 + - - +
69A ASN* 3.0 21.5 - - - +
71A LEU* 1.3 75.6 - - - +
73A LYS* 1.3 56.7 + - + +
75A GLU* 2.7 30.4 + - - +
76A ILE 5.0 1.6 - - - +
78A LEU* 4.4 14.5 - - + +
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Residues in contact with LYS 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* 2.8 53.6 + - - +
70A ALA* 2.8 12.6 + - - +
72A GLU* 1.3 76.0 - - + +
74A GLU* 1.3 59.1 + - + +
75A GLU* 3.1 7.6 + - - +
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 4.9 2.8 - - - +
44A ARG* 3.0 41.4 + - - +
47A LYS* 3.2 22.8 - - + +
48A ARG* 3.1 31.0 + - - +
70A ALA* 2.9 16.0 + - - +
71A LEU* 3.1 12.7 + - - +
72A GLU 3.0 0.4 - - - -
73A LYS* 1.3 78.4 - - + +
75A GLU* 1.3 71.1 + - - +
76A ILE* 3.4 18.6 + - + +
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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
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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