Contacts of the helix formed by residues 64 - 83 (chain A) in PDB entry 6YBO
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 SER 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLY 3.6 3.0 + - - -
63A SER* 1.3 76.2 - - - +
65A ASP* 1.3 60.6 + - - +
66A SER* 3.6 7.4 + - - -
67A GLU* 3.0 37.0 + - - +
68A ARG* 2.8 28.1 + - - +
121A ARG* 5.6 0.2 - - - -
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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
----------------------------------------------------------
63A SER 5.0 0.3 - - - +
64A SER* 1.3 74.8 - - - +
66A SER* 1.3 57.7 + - - +
68A ARG* 3.4 10.3 + - - +
69A GLU* 3.0 28.4 + - - +
121A ARG* 3.2 24.2 + - - -
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 3.2 7.4 + - - -
65A ASP* 1.3 76.2 - - - +
67A GLU* 1.3 66.0 + - - +
69A GLU* 3.3 9.9 + - - +
70A GLU* 3.2 28.6 + - - +
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLY 4.8 0.3 - - - +
63A SER* 3.5 16.8 + - - +
64A SER* 3.0 35.2 + - - +
66A SER* 1.3 76.9 - - - +
68A ARG* 1.3 62.9 - - - +
70A GLU* 3.2 8.2 + - - +
71A HIS* 3.0 38.3 + - + +
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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
----------------------------------------------------------
55A ASP* 6.1 2.6 - - - +
59A ILE* 3.7 49.1 - - + +
63A SER* 4.4 2.3 - - - +
64A SER 2.8 17.7 + - - +
65A ASP* 3.4 9.2 - - - +
67A GLU* 1.3 76.3 - - - +
69A GLU* 1.3 62.8 + - - +
71A HIS* 3.3 3.7 + - - +
72A VAL* 3.0 31.6 + - + +
121A ARG* 3.5 73.6 + - - +
122A ASN* 5.0 2.6 + - - +
125A LEU* 4.1 21.2 - - - +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP 3.0 13.8 + - - +
66A SER* 3.5 12.6 - - - +
67A GLU 3.2 0.4 - - - -
68A ARG* 1.3 78.7 - - - +
70A GLU* 1.3 69.0 + - - +
72A VAL* 3.4 6.0 + - - +
73A LYS* 2.9 41.8 + - + +
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 3.2 17.6 + - - +
67A GLU* 3.2 10.3 + - - +
69A GLU* 1.3 83.0 - - - +
71A HIS* 1.3 66.8 + - + +
73A LYS* 3.4 34.4 + - - +
74A ARG* 3.0 34.4 + - + +
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Residues in contact with HIS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 3.7 25.9 + - + +
59A ILE* 4.3 7.4 - - + -
60A PRO* 3.5 34.2 - - + +
63A SER* 4.4 6.3 + - - -
67A GLU* 3.0 36.5 + - + +
68A ARG* 3.3 7.6 + - - +
70A GLU* 1.3 76.8 - - + +
72A VAL* 1.3 61.5 + - - +
74A ARG* 3.8 17.2 + - - +
75A PHE* 3.2 23.0 + - - +
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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
----------------------------------------------------------
58A LEU* 4.6 6.3 - - + -
59A ILE* 4.0 21.3 - - + -
68A ARG* 3.0 21.7 + - + +
69A GLU* 3.9 5.8 - - - +
71A HIS* 1.3 73.3 - - - +
73A LYS* 1.3 60.4 + - - +
75A PHE* 3.2 6.3 + - + +
76A ARG* 2.8 44.0 + - + +
125A LEU* 4.0 32.1 - - + -
128A GLU* 4.3 12.8 - - - +
129A LEU* 4.7 6.1 - - + -
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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
----------------------------------------------------------
69A GLU* 2.9 31.0 + - + +
70A GLU* 3.4 33.9 + - - +
72A VAL* 1.3 77.2 - - - +
74A ARG* 1.3 63.5 + - + +
76A ARG* 3.3 7.3 + - - +
77A GLN* 3.1 23.4 + - + +
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP* 2.6 42.6 + - - -
36A PRO* 5.2 2.4 - - - +
37A VAL* 3.6 33.2 - - + +
70A GLU* 3.0 25.4 + - + +
71A HIS* 3.8 16.6 + - - +
73A LYS* 1.3 79.1 - - + +
75A PHE* 1.3 62.8 + - - +
77A GLN* 3.4 7.0 + - - +
78A ALA 3.2 16.8 + - - -
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Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.3 17.7 - - + -
36A PRO* 4.3 12.6 - - + -
37A VAL* 4.4 7.8 - - + +
40A VAL* 3.6 26.9 - - + -
51A VAL* 3.9 21.5 - - + -
53A PHE* 4.8 7.4 - + - -
58A LEU* 3.5 37.0 - - + -
71A HIS 3.2 16.5 + - - +
72A VAL* 3.2 5.6 + - - +
74A ARG* 1.3 79.8 - - - +
76A ARG* 1.3 61.6 + - - +
78A ALA* 3.1 4.7 + - - +
79A LEU* 3.0 46.6 + - + +
86A VAL* 4.1 10.1 - - + -
129A LEU* 4.2 17.3 - - + -
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 2.8 28.9 + - + +
73A LYS* 3.8 6.5 - - - +
75A PHE* 1.3 75.2 - - + +
77A GLN* 1.3 58.1 + - - +
79A LEU* 3.3 11.8 + - - +
80A ASP* 2.9 46.3 + - - +
128A GLU* 3.3 43.1 + - - +
129A LEU* 3.6 33.5 + - + +
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Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 3.1 16.9 + - + +
74A ARG* 3.7 7.2 - - - +
75A PHE 3.2 0.2 - - - -
76A ARG* 1.3 78.4 - - - +
78A ALA* 1.3 56.8 + - - +
80A ASP* 3.2 17.0 + - - +
81A ASP* 2.8 68.1 + - - +
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Residues in contact with ALA 78 (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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37A VAL* 3.9 31.0 - - + +
40A VAL* 4.1 21.5 - - + -
41A ARG* 5.1 6.5 - - + +
74A ARG 3.2 11.7 + - - +
75A PHE* 3.1 9.2 + - - +
77A GLN* 1.3 77.0 - - - +
79A LEU* 1.3 60.4 - - - +
81A ASP* 3.3 7.8 + - - +
82A THR* 2.8 33.2 + - - +
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Residues in contact with LEU 79 (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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40A VAL* 4.3 9.0 - - + -
51A VAL* 4.4 5.4 - - + -
75A PHE* 3.0 42.9 + - + +
76A ARG* 3.5 16.4 - - + +
78A ALA* 1.3 75.9 - - - +
80A ASP* 1.3 59.2 + - - +
82A THR* 3.3 3.8 + - - -
83A GLY* 2.8 29.1 + - - -
84A MET* 3.4 37.5 + - + +
85A LYS* 5.8 0.2 - - - -
86A VAL* 3.7 31.9 - - + -
129A LEU* 4.4 13.2 - - + +
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 2.9 33.8 + - - +
77A GLN* 3.6 20.6 + - - +
79A LEU* 1.3 80.0 - - - +
81A ASP* 1.3 63.3 + - - +
82A THR 3.4 0.5 + - - -
83A GLY* 3.9 5.6 + - - -
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Residues in contact with ASP 81 (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 ARG* 4.9 13.8 + - + +
77A GLN* 2.8 50.8 + - - +
78A ALA* 3.7 8.0 - - - +
80A ASP* 1.3 77.9 - - - +
82A THR* 1.3 65.4 + - + +
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Residues in contact with THR 82 (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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40A VAL* 3.6 5.0 - - + +
41A ARG* 4.2 26.0 - - + -
44A ALA* 3.8 29.2 - - + +
78A ALA 2.8 21.0 + - - +
79A LEU 3.4 1.0 + - - -
81A ASP* 1.3 86.0 - - + +
83A GLY* 1.3 58.7 + - - +
84A MET* 3.1 24.5 + - - +
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Residues in contact with GLY 83 (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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49A HIS 4.5 2.1 - - - +
79A LEU 2.8 9.4 + - - -
80A ASP 3.9 4.7 + - - -
81A ASP 3.8 1.0 - - - -
82A THR* 1.3 77.2 - - - +
84A MET* 1.3 64.1 + - - +
85A LYS* 3.6 23.8 + - - +
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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
------------------------------------------------------------
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