Contacts of the helix formed by residues 60 - 78 (chain D) in PDB entry 1S5E
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 60 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ILE* 3.1 19.3 - - - +
59D ASP* 1.3 78.6 - - - +
61D GLN* 1.3 59.7 + - - +
62D LYS 3.3 0.6 + - - -
63D LYS* 4.3 5.6 + - - +
64D ALA* 4.2 7.1 + - - +
34E LYS* 4.5 3.3 + - - +
36E GLU* 2.6 44.9 + - - +
52E VAL* 6.2 0.7 - - - -
53E PRO* 6.4 1.6 - - - -
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Residues in contact with GLN 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLN 4.1 1.2 - - - +
57D HIS* 3.4 22.9 - - + -
58D ILE* 2.8 40.9 + - + +
60D SER* 1.3 77.5 + - - +
62D LYS* 1.3 59.0 + - - +
63D LYS 3.4 0.2 - - - -
64D ALA* 3.1 3.5 + - - +
65D ILE* 2.8 34.7 + - + +
88D TRP* 4.0 2.6 - - - -
751D GAL 3.0 28.0 + - - -
31E LEU* 2.8 28.7 + - - +
32E ALA* 3.9 2.0 - - - +
33E GLY* 3.4 17.6 - - - +
36E GLU* 3.5 19.1 - - - +
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PRO* 4.3 23.0 - - + +
54D GLY 5.4 2.0 - - - +
57D HIS* 4.2 18.2 - - + +
58D ILE 4.1 10.1 - - - +
59D ASP* 3.1 24.5 + - - +
61D GLN* 1.3 79.6 - - - +
63D LYS* 1.3 63.2 + - - +
65D ILE* 3.3 13.9 + - + +
66D GLU* 3.4 17.5 + - - +
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Residues in contact with LYS 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG 5.9 2.9 - - - +
59D ASP 4.5 1.6 + - - -
60D SER 4.3 5.7 + - - +
61D GLN 3.4 0.4 - - - -
62D LYS* 1.3 77.7 - - - +
64D ALA* 1.3 58.0 + - - +
66D GLU* 3.3 8.7 + - - +
67D ARG* 3.0 26.9 + - - +
66E GLU* 4.4 20.5 - - + +
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D SER 4.2 2.6 + - - +
61D GLN 3.1 7.1 + - - +
63D LYS* 1.3 77.1 - - - +
65D ILE* 1.3 59.4 + - - +
67D ARG* 3.2 11.8 + - - +
68D MET* 2.9 30.3 + - - +
29E GLU* 4.7 0.7 - - - +
30E SER 4.2 7.2 - - - +
31E LEU* 3.5 31.4 - - + +
36E GLU* 4.2 19.3 - - + -
66E GLU* 6.0 0.2 - - - -
69E LYS* 6.2 2.0 - - - +
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D VAL* 3.8 19.7 - - + +
51D GLU 4.0 9.9 - - - +
53D PRO* 4.3 17.5 - - + -
57D HIS* 3.7 42.2 - - + +
61D GLN* 2.8 22.0 + - + +
62D LYS* 3.6 11.0 - - + +
64D ALA* 1.3 76.4 - - - +
66D GLU* 1.3 66.4 + - - +
68D MET* 3.3 7.5 + - - +
69D LYS* 3.2 40.2 + - - +
31E LEU* 3.9 20.8 - - + +
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Residues in contact with GLU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 5.9 6.7 - - + -
53D PRO* 4.5 8.8 - - - +
62D LYS 3.4 12.9 + - - +
63D LYS* 3.3 10.0 + - - +
64D ALA 3.3 0.6 - - - -
65D ILE* 1.3 82.5 - - - +
67D ARG* 1.3 61.9 + - - +
69D LYS* 2.9 27.5 + - - +
70D ASP* 3.1 16.3 + - - +
63H LYS* 4.6 33.1 - - + +
67H ARG* 3.0 42.1 + - - +
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 4.5 7.9 - - - +
63D LYS 3.0 13.8 + - - +
64D ALA* 3.2 13.5 + - - +
66D GLU* 1.3 74.8 - - - +
68D MET* 1.3 56.8 + - - +
70D ASP* 3.1 13.7 + - - +
71D THR* 2.8 30.8 + - - -
27E TYR* 4.7 1.7 + - - -
29E GLU* 3.2 31.2 - - - +
66E GLU* 3.0 50.9 + - - +
69E LYS* 3.6 30.6 - - - +
70E ASP* 2.3 41.5 + - - +
73E ARG* 3.9 7.8 - - - +
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Residues in contact with MET 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D VAL* 3.8 22.7 - - + -
64D ALA 2.9 16.1 + - - +
65D ILE* 3.7 5.6 - - - +
66D GLU 3.3 0.2 - - - -
67D ARG* 1.3 77.2 - - - +
69D LYS* 1.3 56.9 + - - +
71D THR* 3.3 2.6 + - - -
72D LEU* 3.0 40.3 + - + +
96D ILE* 3.9 20.0 - - + -
98D ALA* 4.0 3.8 - - - -
99D ILE* 3.7 30.7 - - + -
29E GLU* 3.3 33.1 + - + +
30E SER 5.1 0.4 - - - -
31E LEU* 3.5 29.8 - - + +
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Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D TYR* 3.7 10.2 + - - +
29D GLU* 6.3 0.4 - - + -
36D GLU* 4.2 18.6 + - - +
37D MET* 4.7 3.8 - - - +
38D ALA* 4.0 23.1 - - + +
50D VAL* 3.8 23.8 - - + -
51D GLU 5.2 0.8 + - - +
53D PRO* 4.8 4.8 - - - +
65D ILE* 3.2 27.6 + - - +
66D GLU* 2.9 40.2 + - - +
68D MET* 1.3 72.9 - - - +
70D ASP* 1.3 66.0 + - - +
72D LEU* 3.6 4.3 + - - +
73D ARG* 3.2 23.6 + - - +
67H ARG* 3.6 30.3 + - - +
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Residues in contact with ASP 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 3.0 35.3 + - - +
66D GLU* 3.1 16.4 + - - +
67D ARG* 3.1 14.5 + - - +
69D LYS* 1.3 76.1 - - - +
71D THR* 1.3 62.8 + - - +
73D ARG* 3.3 21.5 + - - +
74D ILE* 3.2 25.2 + - - +
70E ASP* 5.3 0.2 - - - +
73E ARG* 3.7 16.6 + - - +
67H ARG* 2.8 33.2 + - - +
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Residues in contact with THR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ARG 2.8 10.9 + - - -
68D MET* 3.3 10.3 + - - +
70D ASP* 1.3 73.8 - - - +
72D LEU* 1.3 58.0 + - - +
74D ILE* 3.4 3.2 - - - +
75D ALA* 2.8 31.4 + - + +
99D ILE* 4.3 22.7 - - + -
101D MET* 4.3 17.5 - - + -
27E TYR* 4.8 0.9 - - + -
29E GLU* 2.7 37.1 + - - +
73E ARG* 2.9 32.0 + - - +
77E LEU* 5.6 0.2 - - - +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.8 7.3 - - + +
27D TYR* 4.1 15.9 - - + -
38D ALA* 5.3 3.4 - - + -
40D ILE* 4.1 32.5 - - + -
50D VAL* 3.6 30.5 - - + -
68D MET* 3.0 28.0 + - + +
69D LYS* 4.1 2.5 - - - +
71D THR* 1.3 72.8 - - + +
73D ARG* 1.3 65.8 + - - +
75D ALA* 3.8 3.4 - - - +
76D TYR* 2.9 25.1 + - - +
85D LEU* 5.4 0.2 - - + -
96D ILE* 3.8 17.5 - - + -
99D ILE* 3.7 29.6 - - + -
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Residues in contact with ARG 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ASP* 5.0 8.3 + - - -
27D TYR* 3.7 25.9 - - + -
29D GLU* 4.3 3.1 + - - -
69D LYS 3.2 17.3 + - - +
70D ASP* 3.8 25.4 + - - +
71D THR 3.3 0.2 - - - -
72D LEU* 1.3 79.5 - - - +
74D ILE* 1.3 58.9 + - - +
76D TYR* 3.3 3.9 + - - +
77D LEU* 3.0 41.9 + - + +
67H ARG* 3.7 24.7 + - - +
70H ASP* 3.8 15.4 + - - +
71H THR* 2.9 59.7 + - - +
74H ILE* 4.2 13.3 - - - +
101H MET* 4.7 4.9 - - + -
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Residues in contact with ILE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TYR* 4.3 18.2 - - + +
227A GLN* 3.7 37.0 - - + +
70D ASP 3.2 11.5 + - - +
71D THR* 3.4 15.7 - - - +
73D ARG* 1.3 78.0 - - - +
75D ALA* 1.3 67.0 + - - +
77D LEU* 4.4 14.4 - - + +
78D THR* 2.7 44.8 + - + -
73E ARG* 4.2 12.1 - - - +
77E LEU* 3.7 22.4 - - + -
74H ILE* 5.7 1.1 - - + -
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 4.0 16.0 + - + +
71D THR* 2.8 20.0 + - + +
72D LEU* 3.8 5.6 - - - +
74D ILE* 1.3 77.8 - - - +
76D TYR* 1.3 61.7 + - - +
78D THR* 3.5 5.6 + - - -
79D GLU* 3.1 4.2 + - - -
80D ALA* 3.1 35.2 + - + +
82D VAL* 5.2 2.7 - - + -
99D ILE* 5.5 1.8 - - + -
101D MET* 4.0 26.0 - - + -
77E LEU* 4.9 2.9 - - + -
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Residues in contact with TYR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.6 42.2 - - + +
25D PHE 3.5 22.2 - - - -
26D SER* 4.0 3.4 - - - -
27D TYR* 3.7 22.0 - - + -
72D LEU 2.9 14.9 + - - +
73D ARG 3.3 7.4 - - - +
74D ILE 3.2 0.2 - - - -
75D ALA* 1.3 75.9 - - - +
77D LEU* 1.3 84.9 + - + +
79D GLU* 3.1 18.2 + - - +
80H ALA* 5.3 3.1 - - + -
81H LYS 4.8 1.9 + - - -
101H MET* 3.6 26.6 - - + +
102H ALA* 3.1 31.4 + - - -
103H ASN* 3.7 7.6 + - - +
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PHE* 5.0 0.9 - - - -
226A TYR* 4.4 15.6 - - + -
73D ARG* 3.0 30.7 + - + +
74D ILE* 4.0 15.3 - - + +
76D TYR* 1.3 93.3 - - + +
78D THR* 1.3 60.4 + - - +
79D GLU* 3.6 6.2 + - - +
74H ILE* 3.8 41.3 - - + -
75H ALA* 5.2 0.9 - - - -
78H THR* 4.0 11.8 - - + +
80H ALA* 3.8 29.4 - - + -
101H MET* 4.2 8.7 - - + -
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Residues in contact with THR 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 5.7 1.4 - - - -
219A LYS* 6.0 0.2 - - - -
223A PHE* 3.5 62.0 - - + -
226A TYR* 4.4 3.6 - - + -
227A GLN* 5.4 0.2 - - - +
74D ILE* 2.7 44.5 + - + +
75D ALA* 3.5 7.6 + - - -
77D LEU* 1.3 76.6 - - - +
79D GLU* 1.3 69.4 + - - +
80D ALA* 3.2 11.4 + - - +
77E LEU* 3.9 12.2 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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