Contacts of the helix formed by residues 68 - 87 (chain A) in PDB entry 2CT8
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ILE* 1.3 74.4 - - - +
69A PRO* 1.3 75.1 - - - +
70A LYS* 2.9 20.1 + - - +
71A GLU* 3.0 29.2 + - - +
72A LEU* 3.1 11.7 + - - +
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Residues in contact with PRO 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 4.4 5.8 - - + -
59A GLN* 5.0 7.9 - - + +
62A ALA* 4.1 21.8 - - + -
67A ILE 3.6 4.9 - - - +
68A SER* 1.3 87.0 - - - +
70A LYS* 1.3 64.6 + - - +
72A LEU* 3.5 1.9 + - + +
73A VAL* 3.0 27.2 + - - +
215A TRP* 3.7 46.2 - - + +
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Residues in contact with LYS 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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68A SER* 3.3 12.9 + - - +
69A PRO* 1.3 80.6 - - - +
71A GLU* 1.3 59.0 + - - +
73A VAL* 3.0 6.2 + - + +
74A ASP* 2.6 75.4 + - - +
96A ARG* 3.6 15.8 - - - +
98A THR* 4.0 19.5 + - - -
215A TRP* 4.4 14.1 - - + -
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 5.2 5.6 - - + -
68A SER* 3.0 25.0 + - - +
70A LYS* 1.3 80.9 - - - +
72A LEU* 1.3 69.0 + - - +
73A VAL 2.8 0.3 + - - -
74A ASP* 2.9 17.3 + - - +
75A ARG* 2.8 35.5 + - - +
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Residues in contact with LEU 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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16A VAL 4.8 2.4 - - - +
17A ASN* 5.6 1.3 - - - -
58A ILE* 3.7 26.5 - - + +
61A LYS* 4.1 18.8 - - + +
62A ALA* 3.6 30.1 - - + +
65A LEU* 4.5 16.2 - - + -
67A ILE* 4.0 19.1 - - + +
68A SER 3.1 8.3 + - - +
69A PRO* 3.8 9.2 - - + +
71A GLU* 1.3 78.4 - - - +
73A VAL* 1.3 59.7 + - + +
75A ARG* 3.6 11.4 - - - +
76A ASN* 3.2 39.4 + - - +
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Residues in contact with VAL 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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16A VAL* 4.0 10.2 - - + +
53A GLU* 2.8 58.3 - - + +
58A ILE* 3.5 29.8 - - + -
69A PRO 3.0 18.9 + - - +
70A LYS* 3.0 6.9 + - + +
71A GLU 2.8 1.0 + - - -
72A LEU* 1.3 74.5 - - - +
74A ASP* 1.3 64.0 + - - +
75A ARG 3.1 1.3 - - - -
77A ALA* 3.0 28.8 + - - +
96A ARG* 3.3 7.2 - - - +
98A THR* 4.3 4.5 - - + -
215A TRP* 4.3 6.1 - - + -
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Residues in contact with ASP 74 (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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70A LYS* 2.6 62.9 + - - +
71A GLU* 2.9 21.0 + - - +
73A VAL* 1.3 73.2 - - - +
75A ARG* 1.3 62.8 + - - +
77A ALA* 4.0 1.6 - - - +
78A GLU* 3.4 18.7 + - - +
96A ARG* 2.6 26.0 + - - +
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Residues in contact with ARG 75 (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 LEU* 5.8 1.0 - - - +
67A ILE* 3.3 37.4 - - - +
71A GLU* 2.8 20.2 + - - +
72A LEU* 3.6 15.5 - - - +
74A ASP* 1.3 80.4 - - - +
76A ASN* 1.3 72.6 + - - +
78A GLU* 3.4 14.7 + - - +
79A ARG* 3.6 7.4 + - - +
336B LYS* 2.8 46.9 - - - +
496B GLU 4.1 4.9 - - - +
497B GLY* 3.4 18.6 - - - +
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Residues in contact with ASN 76 (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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16A VAL* 2.9 39.7 + - + +
17A ASN 4.8 3.2 - - - -
18A ASP 4.6 11.6 - - - +
19A VAL* 5.1 0.5 - - - +
72A LEU* 3.2 37.3 + - - +
75A ARG* 1.3 76.1 - - - +
77A ALA* 1.3 66.9 + - - +
78A GLU 2.9 2.5 - - - -
79A ARG* 2.7 62.9 + - + +
80A PHE* 3.4 10.0 + - + -
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Residues in contact with ALA 77 (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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16A VAL* 4.0 11.5 - - + +
51A THR* 4.0 9.4 - - - +
53A GLU* 3.2 23.6 - - - +
73A VAL 3.0 21.5 + - - +
74A ASP 4.0 2.5 - - - +
76A ASN* 1.3 78.4 - - - +
78A GLU* 1.3 60.3 + - - +
80A PHE* 3.5 6.1 + - - +
81A LYS* 3.4 25.1 + - - +
94A PHE* 3.9 3.7 - - + -
96A ARG* 3.5 18.4 - - - +
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Residues in contact with GLU 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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74A ASP 3.4 9.9 + - - +
75A ARG* 3.4 12.2 + - - +
76A ASN 2.9 0.4 - - - -
77A ALA* 1.3 77.1 - - - +
79A ARG* 1.3 65.6 + - - +
80A PHE 3.1 2.0 - - - -
81A LYS* 3.1 28.8 + - - +
82A LYS* 2.9 44.1 + - + +
496B GLU* 3.8 27.9 - - + +
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Residues in contact with ARG 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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19A VAL* 4.2 18.5 - - - +
20A PRO* 3.9 23.3 - - + +
75A ARG* 3.6 4.4 + - - +
76A ASN* 2.7 48.7 + - + +
78A GLU* 1.3 77.5 - - - +
80A PHE* 1.3 57.5 + - + +
82A LYS* 3.3 6.4 + - - +
83A LEU* 3.0 27.9 + - - +
307A TYR* 4.0 4.0 + - - -
312B GLU* 3.6 41.2 + - - +
336B LYS* 3.5 12.5 - - - +
495B ARG* 5.6 6.2 - - + +
496B GLU 4.2 15.6 + - - +
497B GLY* 2.9 41.6 + - - -
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Residues in contact with PHE 80 (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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14A TYR* 3.6 33.7 - + + -
15A TYR 3.4 22.0 - - - -
16A VAL* 4.2 4.7 - - + -
18A ASP 4.4 7.9 - - - -
20A PRO* 3.9 32.8 - - + -
24A HIS* 3.9 24.7 - + + -
51A THR* 3.6 20.4 - - + -
76A ASN 3.4 13.4 + - - -
77A ALA 3.7 2.2 - - - +
78A GLU 3.1 0.4 - - - -
79A ARG* 1.3 78.2 - - + +
81A LYS* 1.3 66.2 + - - +
83A LEU* 3.1 4.7 + - + +
84A TRP* 3.0 48.4 + + - +
94A PHE* 3.7 20.9 - - + -
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Residues in contact with LYS 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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77A ALA* 3.4 14.7 + - - +
78A GLU* 3.1 29.7 + - - +
80A PHE* 1.3 76.0 - - - +
82A LYS* 1.3 63.3 + - - +
84A TRP* 3.4 5.9 + - - +
85A GLU* 3.1 22.7 + - - +
91A TYR* 4.5 11.0 + - - +
94A PHE* 3.5 52.7 - - + -
96A ARG* 3.9 21.7 - - - +
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Residues in contact with LYS 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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78A GLU* 2.9 40.0 + - - +
79A ARG 3.6 4.5 - - - +
81A LYS* 1.3 77.8 - - + +
83A LEU* 1.3 57.1 + - - +
85A GLU* 3.3 28.4 + - - +
86A PHE* 2.9 28.4 + - - +
307A TYR* 3.4 10.6 + - - +
494B LYS* 3.3 34.6 + - - +
495B ARG* 4.0 4.3 - - - -
496B GLU* 3.5 32.2 + - + +
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Residues in contact with LEU 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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20A PRO* 3.5 29.6 - - + -
21A HIS 5.0 0.4 - - - +
25A ALA* 4.7 2.2 - - + +
79A ARG 3.0 14.0 + - - +
80A PHE* 3.1 9.2 + - - +
82A LYS* 1.3 74.7 - - - +
84A TRP* 1.3 81.7 + - + +
86A PHE* 3.0 7.8 + - + +
87A LEU* 2.7 50.1 + - + +
306A PRO* 3.8 31.0 - - + -
307A TYR* 3.2 31.3 + - + +
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Residues in contact with TRP 84 (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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14A TYR* 3.5 16.5 - + - -
24A HIS* 3.6 14.1 - - + -
25A ALA* 3.9 12.3 - - - -
28A THR* 3.1 45.1 - - + -
49A THR* 4.0 13.4 + - + -
80A PHE* 3.0 36.5 + + - +
81A LYS* 3.8 3.6 - - - +
83A LEU* 1.3 101.6 - - + +
85A GLU* 1.3 61.3 + - - +
87A LEU* 3.3 7.2 + - + -
88A LYS 3.0 4.7 + - - -
89A ILE* 3.0 43.4 + - + +
91A TYR* 3.7 30.7 - + + -
94A PHE* 3.4 31.4 - + - -
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Residues in contact with GLU 85 (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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81A LYS 3.1 13.7 + - - +
82A LYS* 3.4 33.9 + - - +
83A LEU 3.1 0.2 - - - -
84A TRP* 1.3 77.0 - - - +
86A PHE* 1.3 62.8 + - - +
88A LYS* 3.1 19.0 + - - +
89A ILE 5.1 0.9 - - - +
494B LYS* 6.1 0.7 - - - +
37D A 5.2 7.4 + - - -
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Residues in contact with PHE 86 (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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82A LYS 2.9 13.8 + - - +
83A LEU* 3.4 10.1 - - + +
85A GLU* 1.3 78.3 + - - +
87A LEU* 1.3 70.9 + - + +
88A LYS* 3.2 14.6 + - - +
307A TYR* 3.4 51.1 - + + -
310A VAL* 4.1 23.1 - - + -
311A GLN* 4.2 9.2 - - - -
315A LEU* 4.8 5.1 - - + +
490B ILE* 4.2 21.5 - - + -
493B PRO* 3.4 36.6 - - + -
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Residues in contact with LEU 87 (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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25A ALA* 3.8 29.2 - - + -
29A ILE* 4.4 19.1 - - + -
83A LEU* 2.7 36.9 + - + +
84A TRP* 3.9 16.4 - - + +
86A PHE* 1.3 80.5 - - + +
88A LYS* 1.3 70.6 + - - +
89A ILE* 3.4 13.6 - - + +
306A PRO* 4.9 3.4 - - + -
310A VAL* 3.9 20.4 - - + -
315A LEU* 3.5 40.2 - - + +
318A VAL* 6.1 0.4 - - + -
319A ARG* 4.5 4.2 + - - -
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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