Contacts of the helix formed by residues 60 - 79 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L ILE* 3.1 18.2 - - - +
59L ASP* 1.3 79.3 - - - +
61L GLN* 1.3 58.9 + - - +
62L LYS 3.6 0.3 + - - -
63L LYS* 2.9 39.1 + - - +
64L ALA 4.2 0.2 + - - -
34M LYS* 4.6 1.2 + - - +
36M GLU* 2.6 38.1 + - - +
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Residues in contact with GLN 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L GLN 4.0 3.8 + - - +
57L HIS* 3.2 25.4 - - + -
58L ILE* 2.9 40.0 + - + +
60L SER* 1.3 79.3 + - - +
62L LYS* 1.3 59.0 + - - +
63L LYS 3.3 0.4 - - - -
64L ALA* 2.9 3.7 + - - +
65L ILE* 2.8 35.6 + - + +
88L TRP* 4.1 9.7 - - - -
31M LEU* 2.9 36.4 + - - +
32M ALA* 3.9 2.4 - - - +
33M GLY* 3.3 20.7 - - - +
36M GLU* 3.6 18.2 - - - +
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Residues in contact with LYS 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B HIS* 4.7 7.4 - - + -
53L PRO* 5.1 15.8 - - + +
57L HIS* 5.4 6.1 - - + -
58L ILE 4.2 7.9 - - - +
59L ASP* 3.2 21.2 + - - +
61L GLN* 1.3 77.8 - - - +
63L LYS* 1.3 63.4 + - - +
65L ILE* 3.3 10.9 + - - +
66L GLU* 3.3 27.1 + - - +
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Residues in contact with LYS 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASP* 5.4 0.9 - - - +
233B HIS* 3.7 41.7 + - + +
59L ASP 4.5 1.2 + - - -
60L SER* 2.9 40.6 + - - +
62L LYS* 1.3 78.1 - - - +
64L ALA* 1.3 64.9 + - + +
66L GLU* 3.3 4.0 + - - +
67L ARG* 3.0 25.2 + - - +
36M GLU* 4.6 9.7 - - - +
53M PRO* 4.0 26.6 - - - +
66M GLU* 3.6 39.1 - - + +
69M LYS* 4.5 5.2 - - - +
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Residues in contact with ALA 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L SER 4.4 0.4 - - - +
61L GLN 2.9 8.0 + - - +
63L LYS* 1.3 82.3 - - + +
65L ILE* 1.3 65.5 + - - +
67L ARG* 3.3 10.5 + - + +
68L MET* 3.0 23.9 + - - +
29M GLU* 4.7 0.9 - - - +
30M SER 4.2 3.8 - - - +
31M LEU* 3.5 32.7 - - + +
36M GLU* 4.0 24.2 - - + -
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Residues in contact with ILE 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L VAL* 3.8 19.4 - - + +
51L GLU 3.9 10.5 - - - +
53L PRO* 4.3 14.1 - - + -
57L HIS* 3.5 44.6 - - + +
61L GLN* 2.8 23.1 + - + +
62L LYS* 3.6 11.2 - - + +
64L ALA* 1.3 77.0 - - - +
66L GLU* 1.3 65.4 + - - +
68L MET* 3.3 2.9 + - - +
69L LYS* 3.2 39.0 + - - +
31M LEU* 4.1 25.4 - - + -
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Residues in contact with GLU 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASP* 5.5 0.2 - - - -
232B THR* 4.5 5.4 - - - +
233B HIS* 3.9 32.5 - - + +
63K LYS* 3.5 33.9 - - + +
67K ARG* 2.9 43.3 + - - +
53L PRO* 4.4 2.6 - - - +
62L LYS 3.3 14.3 + - - +
63L LYS 3.6 6.7 - - - +
64L ALA 3.2 0.6 - - - -
65L ILE* 1.3 82.2 - - - +
67L ARG* 1.3 63.4 + - - +
69L LYS* 2.9 28.1 + - - +
70L ASP* 3.1 15.0 + - - -
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Residues in contact with ARG 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASP* 3.2 22.8 + - - +
63L LYS 3.0 13.8 + - - +
64L ALA* 3.6 12.3 - - - +
66L GLU* 1.3 77.4 - - - +
68L MET* 1.3 56.2 + - - +
70L ASP* 3.1 12.4 + - - +
71L THR* 2.9 31.0 + - - -
27M TYR* 4.6 1.9 + - - -
29M GLU* 3.3 32.3 - - - +
66M GLU* 3.1 41.4 + - - +
69M LYS* 3.6 29.4 + - - +
70M ASP* 2.6 42.2 + - - +
73M ARG* 3.9 14.6 - - - +
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Residues in contact with MET 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L VAL* 3.8 22.9 - - + -
64L ALA 3.0 15.9 + - - +
65L ILE 3.7 4.5 - - - +
66L GLU 3.3 0.2 - - - -
67L ARG* 1.3 72.5 - - - +
69L LYS* 1.3 62.5 + - - +
71L THR* 3.1 3.1 + - - -
72L LEU* 2.9 44.7 + - + +
96L ILE* 4.0 23.6 - - + -
97L ALA 4.3 1.6 - - - +
98L ALA* 4.0 6.1 - - - -
99L ILE* 3.9 21.1 - - + -
29M GLU* 3.2 48.2 + - + +
30M SER 4.8 0.2 - - - -
31M LEU* 3.7 24.0 - - + +
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Residues in contact with LYS 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K LYS* 4.7 6.5 - - - +
67K ARG* 3.5 29.2 + - - +
27L TYR* 3.7 11.1 + - - +
29L GLU* 6.2 0.4 - - + -
36L GLU* 3.9 19.6 + - - +
37L MET* 4.5 5.1 - - - +
38L ALA* 4.0 22.2 - - + +
50L VAL* 3.8 22.7 - - + -
51L GLU 5.2 0.6 + - - -
53L PRO* 4.7 2.6 - - - +
65L ILE* 3.2 24.1 + - - +
66L GLU* 2.9 39.2 + - - +
68L MET* 1.3 73.8 - - - +
70L ASP* 1.3 65.1 + - - +
72L LEU* 4.1 4.4 - - - +
73L ARG* 3.1 25.1 + - - +
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Residues in contact with ASP 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE 3.4 10.3 - - - +
231B ASP* 3.3 16.6 - - - +
232B THR* 2.5 44.2 + - - -
67K ARG* 2.7 20.1 + - - +
66L GLU 3.1 12.4 + - - +
67L ARG* 3.1 9.4 + - - +
69L LYS* 1.3 76.5 - - - +
71L THR* 1.3 63.9 + - - +
73L ARG* 3.4 17.7 + - - +
74L ILE* 3.1 24.9 + - - +
73M ARG* 3.7 14.5 + - - +
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Residues in contact with THR 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L ARG 2.9 11.3 + - - -
68L MET* 3.1 6.0 + - - -
70L ASP* 1.3 77.3 - - - +
72L LEU* 1.3 58.1 + - - +
74L ILE* 3.3 3.7 + - - +
75L ALA* 2.8 28.3 + - + +
99L ILE* 4.4 17.7 - - + -
101L MET* 3.9 26.7 - - + -
27M TYR* 4.6 1.3 - - + -
29M GLU* 2.6 33.1 + - - +
73M ARG* 2.9 32.7 + - - +
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Residues in contact with LEU 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L ILE* 4.0 8.6 - - + +
27L TYR* 4.1 16.7 - - + -
38L ALA* 5.3 2.5 - - + -
40L ILE* 4.1 29.8 - - + -
50L VAL* 3.5 31.9 - - + -
68L MET* 2.9 27.5 + - + +
69L LYS* 4.1 2.2 - - - +
71L THR* 1.3 72.8 - - - +
73L ARG* 1.3 67.7 + - - +
75L ALA* 3.8 3.4 - - - +
76L TYR* 3.0 25.6 + - - +
85L LEU* 5.3 0.2 - - + -
96L ILE* 3.7 19.3 - - + -
99L ILE* 3.7 29.8 - - + -
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Residues in contact with ARG 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE* 3.8 24.2 - - - +
232B THR* 4.0 2.2 + - - -
67K ARG* 3.6 22.8 + - - +
70K ASP* 3.8 5.9 - - - +
71K THR* 2.8 56.4 + - + +
74K ILE* 3.6 24.7 - - + +
101K MET* 5.0 1.3 - - + -
27L TYR* 3.7 30.3 - - + +
29L GLU* 4.3 2.7 - - - -
69L LYS 3.1 16.8 + - - +
70L ASP* 3.4 28.0 + - - +
71L THR 3.3 0.2 - - - -
72L LEU* 1.3 78.4 - - - +
74L ILE* 1.3 60.8 + - + +
76L TYR* 3.5 4.2 + - - +
77L LEU* 3.2 38.5 + - + +
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Residues in contact with ILE 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B SER* 3.3 41.3 - - - +
227B GLN* 4.1 11.0 - - + +
228B SER* 3.8 21.1 - - - -
74K ILE* 4.3 14.4 - - + -
70L ASP 3.1 13.9 + - - +
71L THR* 3.5 12.3 - - - +
73L ARG* 1.3 81.0 - - + +
75L ALA* 1.3 61.8 + - - +
76L TYR 3.3 0.4 - - - -
77L LEU* 4.1 15.0 - - + +
78L THR* 2.9 38.2 + - + +
73M ARG* 4.4 6.3 - - - +
77M LEU* 3.8 20.2 - - + -
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Residues in contact with ALA 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L ILE* 4.0 16.6 + - + +
71L THR* 2.8 20.3 + - + +
72L LEU* 3.8 4.3 - - - +
74L ILE* 1.3 74.6 - - - +
76L TYR* 1.3 67.1 + - - +
78L THR* 3.6 5.8 - - - -
79L GLU* 3.0 18.7 + - - -
80L ALA* 3.1 18.4 + - + +
82L VAL* 5.4 0.9 - - + -
99L ILE* 5.3 4.0 - - + -
101L MET* 4.0 26.0 - - + -
77M LEU* 5.2 1.1 - - - -
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Residues in contact with TYR 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG* 3.1 26.2 + - - -
80K ALA* 5.6 1.5 - - + +
81K LYS 4.8 1.7 + - - -
101K MET* 3.4 31.3 - - + +
102K ALA 3.1 23.6 + - - -
103K ASN* 3.0 27.6 + - - -
24L ILE* 3.5 40.4 - - + +
25L PHE 3.5 22.2 - - - -
26L SER 4.3 2.0 - - - -
27L TYR* 3.8 20.6 - - + -
72L LEU 3.0 18.8 + - - +
73L ARG 3.5 3.8 - - - +
75L ALA* 1.3 78.7 - - - +
77L LEU* 1.3 84.9 + - + +
79L GLU* 3.1 10.4 + - - +
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Residues in contact with LEU 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG* 2.9 38.8 + - - +
221B GLN* 4.8 0.3 + - - -
224B SER* 3.2 19.1 - - - +
74K ILE* 3.4 33.9 - - + -
75K ALA 5.2 1.3 - - - +
78K THR* 4.3 5.4 - - - +
80K ALA* 3.6 29.8 - - + -
101K MET* 4.3 10.3 - - + -
73L ARG* 3.2 26.6 + - + +
74L ILE* 4.0 9.6 - - + +
75L ALA 3.3 0.2 - - - -
76L TYR* 1.3 95.5 - - + +
78L THR* 1.3 58.9 + - - +
79L GLU* 3.3 2.3 + - - +
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Residues in contact with THR 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TYR* 5.3 0.2 - - - -
221B GLN* 2.8 35.1 + - - +
224B SER* 3.6 24.9 - - - +
225B GLY* 3.6 18.4 - - - +
74L ILE* 2.9 27.1 + - + +
75L ALA* 3.4 7.4 + - - -
77L LEU* 1.3 75.0 - - - +
79L GLU* 1.3 66.0 + - - +
80L ALA* 3.3 16.6 + - - +
77M LEU* 3.8 20.2 - - + +
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Residues in contact with GLU 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TYR* 4.0 23.3 + - + -
217B LYS 5.7 0.9 - - - +
220B ARG* 3.8 33.7 + - - +
221B GLN* 4.5 5.2 + - - +
103K ASN 4.9 2.4 - - - +
23L LYS* 2.6 54.6 + - + +
75L ALA 3.0 8.0 + - - -
76L TYR* 3.1 4.9 + - - +
77L LEU 4.0 2.4 - - - +
78L THR* 1.3 79.9 - - - +
80L ALA* 1.3 65.8 + - - +
81L LYS* 3.5 2.3 + - - -
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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