Contacts of the helix formed by residues 68 - 85 (chain B) in PDB entry 2D68
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 THR 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LEU* 5.5 1.0 - - - +
64B LYS 3.4 15.7 - - - +
65B PHE* 2.6 21.7 + - + +
66B LEU 3.7 0.5 - - - +
67B ASN* 1.3 82.9 - - - +
69B LYS* 1.3 64.1 + - - +
70B ASP* 4.3 4.1 - - - +
71B GLY* 3.0 15.4 + - - -
72B ARG* 2.9 26.7 + - - +
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Residues in contact with LYS 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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67B ASN 4.4 0.2 + - - -
68B THR* 1.3 73.0 - - - +
70B ASP* 1.3 70.9 + - - +
72B ARG* 3.4 5.3 + - - +
73B LEU* 3.1 25.1 + - + +
113B ASP* 5.3 8.7 - - - +
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Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 3.7 18.6 - - + -
132A ILE* 4.0 21.8 - - + +
133A ARG* 3.6 31.1 - - - +
68B THR* 3.3 4.3 + - - +
69B LYS* 1.3 86.0 - - - +
71B GLY* 1.3 57.7 + - - +
73B LEU* 3.2 7.6 + - - +
74B VAL* 2.9 33.6 + - - +
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Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 4.4 0.8 - - - +
65B PHE* 3.1 45.9 - - - -
66B LEU* 4.5 0.7 - - - -
68B THR* 3.0 19.6 + - - -
70B ASP* 1.3 76.1 - - - +
72B ARG* 1.3 59.7 + - - +
74B VAL 3.3 0.5 + - - -
75B ALA* 2.9 26.9 + - - +
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Residues in contact with ARG 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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65B PHE 3.9 1.6 + - - -
66B LEU* 3.7 32.9 + - + +
68B THR 2.9 18.0 + - - +
69B LYS* 3.9 5.2 - - - +
71B GLY* 1.3 76.7 - - - +
73B LEU* 1.3 53.3 + - - +
75B ALA* 3.9 0.7 - - - +
76B SER* 2.7 38.0 + - - -
100B THR* 5.6 1.4 - - - +
103B GLY 4.1 11.7 + - - -
104B LEU* 3.7 28.2 - - + +
105B GLU* 2.7 39.9 + - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 3.8 22.2 - - + -
69B LYS* 3.1 16.6 + - + +
70B ASP* 3.4 11.0 - - - +
71B GLY 3.2 0.2 - - - -
72B ARG* 1.3 74.9 - - - +
74B VAL* 1.3 66.0 + - - +
76B SER* 3.3 3.1 + - - -
77B LEU* 2.9 42.0 + - + +
110B LEU* 3.5 33.4 - - + +
113B ASP* 4.6 20.9 - - + +
114B LEU* 3.9 27.1 - - + -
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 3.7 29.2 - - + -
126A PRO* 4.7 0.4 - - + -
128A LEU* 3.8 33.4 - - + +
129A LEU* 3.9 11.7 - - - +
132A ILE* 3.7 24.7 - - + -
65B PHE* 3.7 10.3 - - + -
70B ASP 2.9 22.6 + - - +
71B GLY 3.6 7.2 - - - +
73B LEU* 1.3 72.2 - - - +
75B ALA* 1.3 63.4 + - - +
77B LEU* 3.1 12.4 + - - +
78B VAL* 3.0 21.5 + - - +
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Residues in contact with ALA 75 (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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81A PHE* 4.0 25.6 - - + -
66B LEU* 3.3 34.1 - - + -
71B GLY 2.9 8.6 + - - +
72B ARG 4.0 1.3 - - - +
74B VAL* 1.3 76.8 - - - +
76B SER* 1.3 58.2 + - - +
78B VAL* 3.2 4.7 + - - +
79B ALA* 2.9 24.8 + - - +
94B PHE* 4.3 5.1 - - + -
98B THR* 6.6 0.2 - - + -
104B LEU* 3.6 17.1 - - + +
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Residues in contact with SER 76 (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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72B ARG 2.7 25.2 + - - -
73B LEU 3.6 0.7 - - - -
75B ALA* 1.3 76.2 - - - +
77B LEU* 1.3 57.0 + - - +
79B ALA* 3.3 3.0 + - - +
80B GLU* 2.9 29.3 + - - +
104B LEU* 3.3 27.4 - - - +
105B GLU* 3.3 24.9 + - - +
110B LEU* 3.4 31.1 - - - +
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Residues in contact with LEU 77 (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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128A LEU* 5.2 0.9 - - + -
132A ILE* 3.7 33.7 - - + -
73B LEU* 2.9 27.4 + - + +
74B VAL* 3.1 7.8 + - - +
76B SER* 1.3 76.1 - - - +
78B VAL* 1.3 58.1 + - - +
80B GLU* 3.3 4.5 + - - +
81B PHE* 3.0 27.9 + - - +
110B LEU* 4.0 11.4 - - + -
114B LEU* 4.0 12.8 - - + -
127B LEU* 3.9 39.9 - - + -
128B LEU* 3.6 37.8 - - + +
131B VAL* 4.7 2.0 - - + -
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 3.9 28.0 - - + -
81A PHE* 3.9 30.1 - - + -
82A LEU* 4.7 3.1 - - + -
128A LEU* 3.7 22.4 - - + -
74B VAL 3.0 14.3 + - - +
75B ALA* 3.2 9.1 + - - +
77B LEU* 1.3 72.8 - - - +
79B ALA* 1.3 65.8 + - - +
81B PHE* 3.1 7.4 + - - +
82B LEU* 3.1 26.0 + - + +
94B PHE* 4.1 20.9 - - + -
128B LEU* 4.4 4.7 - - + -
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Residues in contact with ALA 79 (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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75B ALA 2.9 13.7 + - - +
76B SER* 3.7 7.4 - - - +
78B VAL* 1.3 76.2 - - - +
80B GLU* 1.3 57.9 + - - +
82B LEU* 3.1 13.9 + - - +
83B GLN* 2.9 40.2 + - - +
91B LEU* 4.5 10.0 - - + +
94B PHE* 4.0 17.9 - - + -
95B GLN* 6.0 1.3 - - - +
104B LEU* 4.2 14.8 - - + +
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Residues in contact with GLU 80 (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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76B SER 2.9 17.6 + - - +
77B LEU* 3.7 6.6 - - - +
78B VAL 3.2 0.2 - - - -
79B ALA* 1.3 72.7 - - - +
81B PHE* 1.3 62.5 + - - +
83B GLN* 3.3 9.4 + - + +
84B PHE* 2.8 36.0 + - - +
105B GLU 5.6 0.9 - - - +
107B ARG* 2.9 63.5 + - + +
110B LEU* 4.4 9.4 - - + -
126B PRO* 3.6 4.6 - - - +
127B LEU* 2.8 29.2 + - + +
128B LEU 4.5 1.2 + - - -
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Residues in contact with PHE 81 (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 LEU* 4.2 12.1 - - + -
65A PHE* 3.7 16.8 - + - -
74A VAL* 3.7 22.4 - - + -
75A ALA* 4.5 15.5 - - + -
78A VAL* 3.9 21.3 - - + -
94A PHE* 4.2 15.9 - + - -
98A THR* 5.4 0.9 - - + -
77B LEU 3.0 12.9 + - - +
78B VAL 3.3 8.7 - - - +
80B GLU* 1.3 77.3 + - - +
82B LEU* 1.3 72.0 + - + +
84B PHE* 3.3 3.3 + - - +
85B PHE* 3.3 46.7 + + - +
87B LEU* 3.9 19.3 - - + -
126B PRO* 4.0 22.4 - - + -
128B LEU* 4.3 4.7 - - + -
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Residues in contact with LEU 82 (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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78A VAL* 4.8 4.0 - - + -
82A LEU* 5.9 2.0 - - + -
90A THR* 5.3 0.7 - - + -
94A PHE* 4.1 12.3 - - + -
78B VAL* 3.1 18.1 + - + +
79B ALA* 3.1 8.0 + - - +
81B PHE* 1.3 84.1 - - + +
83B GLN* 1.3 61.7 + - - +
85B PHE 3.5 0.5 + - - -
86B ASN 3.3 2.6 + - - -
87B LEU* 2.9 59.8 + - + +
90B THR* 3.8 30.7 - - + -
91B LEU* 4.3 17.0 - - + -
94B PHE* 4.0 34.1 - - + -
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Residues in contact with GLN 83 (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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79B ALA* 2.9 28.5 + - - +
80B GLU* 3.8 8.2 - - + +
82B LEU* 1.3 74.4 - - - +
84B PHE* 1.3 65.9 + - - +
86B ASN* 3.0 22.3 + - - +
88B ASP* 5.3 4.2 - - - +
91B LEU* 3.7 30.9 - - + +
95B GLN* 5.4 3.6 + - - -
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Residues in contact with PHE 84 (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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61A SER* 4.9 4.9 - - - -
80B GLU* 2.8 28.3 + - - +
81B PHE 3.3 5.1 + - - +
83B GLN* 1.3 73.9 - - - +
85B PHE* 1.3 80.7 + + - +
86B ASN* 3.6 8.1 + - - +
107B ARG* 3.6 20.2 - - - -
123B VAL 3.7 12.8 - - - -
124B GLY* 3.4 13.2 - - - -
125B GLY* 3.4 31.2 - - - -
126B PRO* 3.7 28.5 - - + -
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Residues in contact with PHE 85 (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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59A ASN* 2.8 30.8 + - - +
61A SER* 3.5 26.9 - - - -
62A LEU* 3.8 34.8 - - + -
65A PHE* 3.4 33.0 - + + -
81B PHE* 3.3 45.3 + + - +
83B GLN 3.2 0.6 - - - -
84B PHE* 1.3 103.4 - + - +
86B ASN* 1.3 69.7 - - - +
87B LEU* 3.2 20.5 + - + +
125B GLY* 5.7 0.2 - - - -
126B PRO* 3.8 10.1 - - + -
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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