Contacts of the helix formed by residues 68 - 87 (chain B) in PDB entry 2CSX
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 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ALA* 3.9 2.9 - - - +
67B ILE* 1.3 76.7 - - - +
69B PRO* 1.3 78.0 - - - +
70B LYS* 4.3 6.7 + - - +
71B GLU* 3.0 28.1 + - - +
72B LEU 3.1 10.6 + - - -
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Residues in contact with PRO 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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58B ILE* 3.6 4.9 - - + +
59B GLN* 4.2 15.9 - - + +
62B ALA* 3.6 21.1 - - + -
67B ILE 4.5 0.4 - - - +
68B SER* 1.3 87.2 - - - +
70B LYS* 1.3 62.1 + - - +
72B LEU* 3.3 2.6 + - - +
73B VAL* 3.0 24.1 + - - +
215B TRP* 3.3 49.4 - - + +
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B SER* 3.2 6.7 + - - +
69B PRO* 1.3 78.9 - - - +
71B GLU* 1.3 53.7 + - - +
73B VAL* 3.4 3.3 + - + +
74B ASP* 2.7 78.9 + - - +
96B ARG* 4.1 9.1 - - - +
98B THR* 4.4 21.5 + - + -
215B TRP* 3.6 28.8 - - + -
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Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.9 25.6 - - + -
68B SER* 3.0 27.7 + - - +
70B LYS* 1.3 75.2 - - - +
72B LEU* 1.3 68.4 + - - +
74B ASP* 3.2 13.6 + - - +
75B ARG* 3.2 39.5 + - - +
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Residues in contact with LEU 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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17B ASN* 4.1 16.2 - - - +
58B ILE* 3.4 37.9 - - + +
61B LYS* 4.2 7.2 - - + -
62B ALA* 3.8 15.7 - - + +
65B LEU* 4.6 10.5 - - + -
67B ILE* 3.9 21.7 - - + +
68B SER 3.1 7.5 + - - +
69B PRO 3.6 7.0 - - - +
71B GLU* 1.3 80.6 - - - +
73B VAL* 1.3 66.6 + - - +
75B ARG* 2.9 17.8 + - + +
76B ASN* 3.0 41.2 + - - +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 3.7 12.5 - - + +
53B GLU* 2.9 51.8 - - + +
58B ILE* 3.1 29.4 - - + -
69B PRO 3.0 10.0 + - - +
70B LYS* 3.5 9.4 - - + +
72B LEU* 1.3 81.4 - - - +
74B ASP* 1.3 64.4 + - - +
76B ASN* 3.0 6.9 + - - +
77B ALA* 2.8 26.7 + - - +
96B ARG* 3.1 10.5 - - - +
98B THR* 4.0 7.0 - - + -
215B TRP* 4.6 1.3 - - - +
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Residues in contact with ASP 74 (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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70B LYS* 2.7 55.4 + - - +
71B GLU* 3.5 16.8 - - - +
72B LEU 3.2 0.4 + - - -
73B VAL* 1.3 74.8 - - - +
75B ARG* 1.3 62.7 + - - +
77B ALA* 4.1 1.6 - - - +
78B GLU* 3.4 21.5 + - - +
96B ARG* 2.7 38.6 + - - +
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Residues in contact with ARG 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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65B LEU* 5.4 6.5 - - - +
67B ILE* 3.4 36.3 - - - +
71B GLU* 3.2 27.7 + - - +
72B LEU* 2.9 12.9 + - + +
74B ASP* 1.3 80.4 - - - +
76B ASN* 1.3 68.1 + - - +
78B GLU* 3.6 14.0 - - - +
79B ARG* 3.7 13.8 - - + +
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Residues in contact with ASN 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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16B VAL* 3.5 25.6 - - + +
17B ASN* 3.2 31.5 + - - +
72B LEU* 3.0 41.9 + - - +
73B VAL 3.5 6.3 - - - +
75B ARG* 1.3 77.6 - - - +
77B ALA* 1.3 69.9 + - - +
78B GLU 3.1 1.6 - - - -
79B ARG* 2.7 46.7 + - - +
80B PHE* 3.7 5.6 + - - -
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Residues in contact with ALA 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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16B VAL* 4.3 3.2 - - + +
51B THR* 4.0 20.9 - - + +
53B GLU* 3.2 27.1 - - - +
73B VAL 2.8 14.1 + - - +
74B ASP 4.1 2.0 - - - +
76B ASN* 1.3 71.2 - - - +
78B GLU* 1.3 61.6 + - - +
80B PHE* 3.0 19.3 + - - +
81B LYS* 3.4 15.2 + - - +
94B PHE* 4.2 3.7 - - + -
96B ARG* 3.9 18.6 - - - +
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Residues in contact with GLU 78 (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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74B ASP 3.4 17.1 + - - +
75B ARG* 3.6 9.6 - - - +
76B ASN 3.0 0.4 + - - -
77B ALA* 1.3 78.4 - - - +
79B ARG* 1.3 60.8 + - + +
81B LYS* 3.4 27.0 + - - +
82B LYS* 2.9 59.3 + - + +
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Residues in contact with ARG 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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16B VAL 4.3 0.4 + - - -
17B ASN 3.3 24.9 + - - -
18B ASP 3.9 3.6 + - - -
19B VAL* 3.4 36.3 - - - +
20B PRO* 4.2 18.0 - - + +
75B ARG* 3.7 11.9 - - - +
76B ASN* 2.7 41.7 + - - +
78B GLU* 1.3 70.9 - - + +
80B PHE* 1.3 63.8 + - - +
82B LYS* 3.2 10.0 + - - +
83B LEU* 3.0 21.5 + - - +
307B TYR* 4.4 2.1 + - - -
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Residues in contact with PHE 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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14B TYR* 3.9 19.7 - + + -
15B TYR 4.2 2.7 - - - -
16B VAL* 3.7 21.1 - - - -
18B ASP 3.7 25.1 - - - -
20B PRO* 3.3 24.0 - - + -
24B HIS* 3.6 35.9 - + + -
51B THR* 3.9 18.2 - - + -
76B ASN 4.1 10.8 - - - -
77B ALA* 3.0 7.9 + - - +
79B ARG* 1.3 75.1 - - - +
81B LYS* 1.3 66.6 + - - +
83B LEU* 2.9 4.8 + - - +
84B TRP* 2.9 48.7 + + - +
94B PHE* 4.1 14.6 - - + -
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Residues in contact with LYS 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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77B ALA* 3.4 13.4 + - - +
78B GLU* 3.7 27.5 + - - +
79B ARG 3.3 0.4 - - - -
80B PHE* 1.3 75.8 - - - +
82B LYS* 1.3 59.0 + - + +
84B TRP* 3.0 8.0 + - - +
85B GLU* 2.8 30.4 + - - +
91B TYR* 4.3 16.2 + - - +
94B PHE* 3.8 41.8 - - + +
96B ARG* 4.6 19.4 - - - +
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Residues in contact with LYS 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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78B GLU* 2.9 45.4 + - + +
79B ARG* 3.4 10.5 - - - +
81B LYS* 1.3 78.6 - - + +
83B LEU* 1.3 55.5 + - - +
85B GLU* 3.4 24.0 + - - +
86B PHE* 2.9 27.9 + - - +
307B TYR* 3.5 10.9 + - - +
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Residues in contact with LEU 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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20B PRO* 3.3 32.1 - - + -
21B HIS 4.9 0.9 - - - +
25B ALA* 4.6 2.0 - - + -
79B ARG 3.0 11.3 + - - +
80B PHE 2.9 9.0 + - - +
82B LYS* 1.3 72.2 - - - +
84B TRP* 1.3 86.8 + - + +
86B PHE* 3.1 7.9 + - + +
87B LEU* 2.7 51.4 + - + +
306B PRO* 3.8 28.9 - - + -
307B TYR* 3.4 27.3 + - + +
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Residues in contact with TRP 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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14B TYR* 3.8 17.1 - + - -
24B HIS* 3.7 22.0 - - + -
25B ALA* 3.8 7.0 - - - -
28B THR* 3.1 30.5 - - + -
49B THR* 4.0 23.4 + - + -
50B GLY 6.0 0.2 + - - -
80B PHE* 2.9 33.1 + + - +
81B LYS* 3.5 6.1 - - - +
83B LEU* 1.3 104.4 - - + +
85B GLU* 1.3 57.0 + - - +
87B LEU* 3.5 16.9 - - + -
88B LYS 2.9 23.2 + - - -
89B ILE* 2.9 27.7 + - + +
91B TYR* 3.7 23.6 - + + -
94B PHE* 4.0 27.5 - + - -
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Residues in contact with GLU 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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81B LYS 2.8 16.2 + - - +
82B LYS* 3.5 26.0 - - - +
84B TRP* 1.3 75.8 - - - +
86B PHE* 1.3 62.6 + - - +
88B LYS* 3.1 19.3 + - - +
89B ILE 5.9 0.2 - - - -
91B TYR* 5.3 2.6 + - - +
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Residues in contact with PHE 86 (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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301A GLY 4.1 18.6 - - - -
308A GLU* 6.2 0.9 - - - -
82B LYS 2.9 14.6 + - - +
83B LEU* 3.3 11.9 - - + +
85B GLU* 1.3 79.0 - - - +
87B LEU* 1.3 69.9 + - + +
88B LYS* 3.2 7.7 + - - +
306B PRO 3.9 2.0 - - - -
307B TYR* 3.6 56.1 - + + -
310B VAL* 3.7 34.9 - - + +
311B GLN* 4.6 5.4 - - + -
315B LEU* 4.1 9.0 - - - +
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Residues in contact with LEU 87 (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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25B ALA* 3.7 17.7 - - + -
29B ILE* 5.0 12.3 - - + -
83B LEU* 2.7 41.6 + - + +
84B TRP* 3.6 24.5 - - + -
85B GLU 3.2 0.2 - - - -
86B PHE* 1.3 78.8 - - + +
88B LYS* 1.3 72.0 + - - +
89B ILE* 3.9 21.3 - - + +
306B PRO* 4.8 2.9 - - + -
310B VAL* 3.9 18.2 - - + -
315B LEU* 3.2 38.8 - - + +
318B VAL* 5.8 0.4 - - + -
319B ARG* 4.6 6.6 + - - -
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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