Contacts of the helix formed by residues 60 - 74 (chain B) 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 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B LEU* 1.3 76.0 - - - +
61B GLY* 1.3 67.4 + - - +
63B THR* 3.2 0.3 + - - -
64B GLY* 2.8 10.1 + - - -
82B GLU* 3.3 10.8 - - - -
83B VAL* 3.6 3.3 - - - +
85B GLY 2.8 23.6 - - - -
87B THR* 2.7 29.0 + - - +
106B PRO* 6.0 0.4 - - - +
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLY* 1.3 68.6 - - - +
62B PHE* 1.3 55.0 + - - -
63B THR 2.8 6.1 - - - -
64B GLY 2.6 24.4 + - - -
65B ALA* 3.1 8.5 + - - +
82B GLU* 4.5 4.4 + - - -
83B VAL 4.8 0.4 + - - -
84B GLU 5.4 1.0 + - - -
85B GLY 3.2 4.6 + - - -
86B ASP* 2.9 26.7 + - - -
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Residues in contact with PHE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.9 15.9 - - + -
33A LYS* 3.3 35.7 - - + -
62A PHE* 4.1 27.2 - + + +
66A TYR* 3.4 50.9 - + + -
61B GLY* 1.3 71.4 - - - -
63B THR* 1.3 78.8 + - + +
65B ALA* 3.3 11.8 + - + +
66B TYR* 3.1 21.1 + - - +
86B ASP* 3.9 13.9 - - - -
89B ILE* 5.4 2.5 - - + -
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Residues in contact with THR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 3.7 25.4 - - - +
62A PHE* 5.4 0.2 - - + -
11B ILE* 3.6 26.7 - - + +
60B GLY 3.2 9.2 + - - -
61B GLY 2.8 1.6 + - - -
62B PHE* 1.3 95.6 - - + +
64B GLY* 1.3 66.1 + - - +
66B TYR* 3.3 5.2 + - - +
67B VAL* 3.2 24.1 + - - +
86B ASP* 3.8 4.2 + - - -
87B THR* 2.7 30.2 + - - +
89B ILE* 3.9 11.0 - - + -
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Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.9 12.4 - - - +
60B GLY 2.8 25.7 + - - -
61B GLY 2.6 12.6 + - - -
63B THR* 1.3 69.6 + - - +
65B ALA* 1.3 62.6 + - - -
67B VAL* 3.2 6.2 + - - +
68B ARG* 3.0 25.8 + - - +
87B THR* 3.4 14.3 + - - -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLY 3.1 6.3 + - - +
62B PHE* 3.4 16.4 - - - +
64B GLY* 1.3 75.0 - - - +
66B TYR* 1.3 63.5 + - - +
68B ARG* 3.2 14.5 + - - +
69B ASN* 2.9 25.3 + - - +
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.8 41.7 - + + -
11B ILE* 3.2 46.0 - - + -
33B LYS* 2.7 37.3 + - + -
34B GLN* 3.0 17.1 - - - -
35B PRO* 4.0 9.6 - - + +
62B PHE 3.1 10.3 + - - +
63B THR 3.3 7.2 - - - +
64B GLY 3.2 0.2 - - - -
65B ALA* 1.3 78.8 - - - +
67B VAL* 1.3 78.1 + - - +
69B ASN* 3.0 12.7 + - - +
70B ALA* 3.0 31.4 + - + +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 5.2 0.2 - - + -
10B SER* 3.8 22.9 - - - +
11B ILE* 4.0 11.0 - - + -
35B PRO* 4.1 10.9 - - + +
40B ILE* 3.8 28.0 - - + -
59B LEU* 4.1 17.0 - - + -
63B THR 3.2 14.8 + - - +
64B GLY* 3.4 10.8 - - - +
66B TYR* 1.3 83.1 - - + +
68B ARG* 1.3 64.1 + - - +
70B ALA* 3.3 2.3 + - - +
71B LEU* 3.1 32.9 + - + +
80B PHE* 5.2 0.2 - - + -
87B THR* 4.5 7.2 - - + -
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Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 4.3 27.9 - - + +
64B GLY 3.0 10.8 + - - +
65B ALA* 3.5 14.4 - - - +
67B VAL* 1.3 83.7 - - - +
69B ASN* 1.3 62.1 + - - +
71B LEU* 3.5 3.8 + - - +
72B GLU* 3.0 52.2 + - - +
78B LEU* 3.8 17.2 - - + +
80B PHE* 5.4 7.8 + - + +
82B GLU* 4.3 32.7 + - - +
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Residues in contact with ASN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA 2.9 16.5 + - - +
66B TYR* 3.6 16.0 + - - +
68B ARG* 1.3 73.9 - - - +
70B ALA* 1.3 70.5 + - - +
72B GLU* 3.3 14.2 + - - +
73B LYS* 3.1 37.6 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PRO* 4.3 22.9 - - + -
66B TYR* 3.0 27.0 + - + +
67B VAL* 3.6 4.7 - - - +
69B ASN* 1.3 82.9 - - - +
71B LEU* 1.3 65.0 + - - +
73B LYS* 3.3 6.1 + - - +
74B GLU* 3.2 29.2 + - + +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PRO* 4.0 12.3 - - + -
40B ILE* 4.1 13.2 - - + +
43B SER* 6.1 0.7 - - - -
44B ARG* 3.8 35.9 - - + -
55B ALA* 5.3 5.4 - - + -
67B VAL* 3.1 34.0 + - + +
68B ARG* 4.1 4.7 - - - +
70B ALA* 1.3 73.6 - - - +
72B GLU* 1.3 63.8 + - - +
74B GLU* 3.2 6.8 + - - +
75B GLU 3.1 4.2 + - - -
76B ILE* 2.9 49.2 + - + +
78B LEU* 4.7 7.0 - - + -
80B PHE* 4.2 25.6 - - + -
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ARG* 3.0 48.9 + - - +
69B ASN* 3.6 11.8 - - - +
70B ALA 3.2 0.2 - - - -
71B LEU* 1.3 77.4 - - - +
73B LYS* 1.3 63.7 + - + +
75B GLU* 3.2 17.3 + - - +
76B ILE 4.7 3.6 - - - +
78B LEU* 3.6 26.1 - - + +
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASN* 3.1 31.4 + - - +
70B ALA* 3.6 9.6 - - - +
71B LEU 3.1 0.4 - - - -
72B GLU* 1.3 75.8 - - + +
74B GLU* 1.3 59.0 + - + +
75B GLU* 2.7 21.6 + - - +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PRO* 5.7 1.6 - - - -
44B ARG* 3.1 52.2 + - - +
47B LYS* 3.5 21.5 - - + +
48B ARG* 3.9 15.0 + - - -
70B ALA* 3.2 15.7 + - - +
71B LEU* 3.2 10.3 + - - +
73B LYS* 1.3 75.8 - - + +
75B GLU* 1.3 68.1 + - - +
76B ILE* 3.2 15.3 + - + +
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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