Contacts of the helix formed by residues 58 - 78 (chain K) 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 ILE 58 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K GLN 5.4 1.8 - - - +
57K HIS* 1.3 77.4 - - - +
59K ASP* 1.3 62.3 + - - +
60K SER* 3.2 23.6 - - - +
61K GLN* 2.8 43.2 + - + +
62K LYS* 3.6 6.9 + - - +
33L GLY* 4.1 4.0 - - - -
34L LYS* 4.0 25.1 - - + +
36L GLU* 3.8 7.4 - - - +
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Residues in contact with ASP 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58K ILE* 1.3 72.9 - - - +
60K SER* 1.3 57.8 + - - +
62K LYS* 3.0 44.7 + - - +
63K LYS* 4.1 2.1 + - - +
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Residues in contact with SER 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58K ILE* 3.2 18.7 - - - +
59K ASP* 1.3 78.9 - - - +
61K GLN* 1.3 58.3 + - - +
62K LYS 3.2 0.6 + - - -
63K LYS* 3.3 41.5 + - - +
64K ALA 3.9 0.5 + - - -
34L LYS* 4.7 0.5 + - - -
36L GLU* 2.6 37.1 + - - +
52L VAL* 6.2 0.4 - - - -
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Residues in contact with GLN 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K GLN 4.1 4.0 - - - +
57K HIS* 3.2 32.0 - - + -
58K ILE* 2.8 40.1 + - + +
60K SER* 1.3 77.1 + - - +
62K LYS* 1.3 59.1 + - - +
64K ALA* 3.5 7.8 - - - +
65K ILE* 2.8 34.9 + - + +
88K TRP* 4.3 14.3 - - - -
31L LEU* 3.0 29.4 + - - +
32L ALA* 4.1 1.8 - - - +
33L GLY* 3.5 18.1 - - - +
36L GLU* 3.6 14.1 - - - +
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Residues in contact with LYS 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53K PRO* 4.1 28.9 - - + -
54K GLY* 4.4 8.2 + - - +
57K HIS* 3.9 30.6 + - + -
58K ILE 3.9 7.0 - - - +
59K ASP* 3.0 38.6 + - - +
61K GLN* 1.3 81.2 - - - +
63K LYS* 1.3 63.3 + - - +
65K ILE* 3.4 7.3 + - + +
66K GLU* 3.4 25.0 + - - +
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Residues in contact with LYS 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 4.6 8.6 - - + +
59K ASP 4.1 1.8 + - - +
60K SER* 3.3 37.0 + - - +
62K LYS* 1.3 77.6 - - - +
64K ALA* 1.3 61.8 + - - +
66K GLU* 3.3 8.7 + - - +
67K ARG* 3.0 26.4 + - - +
36L GLU* 4.9 6.6 - - - +
53L PRO* 4.2 25.0 - - - +
66L GLU* 3.5 38.6 - - + +
69L LYS* 4.7 5.2 - - - +
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Residues in contact with ALA 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60K SER 4.1 0.7 - - - +
61K GLN 3.2 11.8 + - - +
63K LYS* 1.3 81.4 - - + +
65K ILE* 1.3 60.2 + - - +
67K ARG* 3.6 10.5 - - - +
68K MET* 2.9 29.6 + - - +
29L GLU* 5.2 0.5 - - - +
30L SER 4.4 2.9 - - - +
31L LEU* 3.5 30.6 - - + +
36L GLU* 4.1 20.9 - - + -
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Residues in contact with ILE 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50K VAL* 3.7 21.9 - - + +
51K GLU 4.0 9.9 - - - +
53K PRO* 4.6 10.8 - - + -
57K HIS* 3.3 44.2 - - + +
61K GLN* 2.8 27.4 + - + +
62K LYS* 3.7 13.2 - - + +
64K ALA* 1.3 72.3 - - - +
66K GLU* 1.3 70.7 + - - +
68K MET* 3.3 7.3 + - - +
69K LYS* 3.1 38.2 + - - +
31L LEU* 4.3 16.8 - - + -
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Residues in contact with GLU 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 5.2 4.9 - - + -
63J LYS* 4.6 33.0 - - + +
67J ARG* 3.0 41.7 + - - +
53K PRO* 4.5 9.2 - - - +
62K LYS 3.4 14.4 + - - +
63K LYS* 3.3 9.7 + - - +
64K ALA 3.2 0.2 - - - -
65K ILE* 1.3 83.9 - - - +
67K ARG* 1.3 62.1 + - - +
69K LYS* 2.8 30.4 + - - +
70K ASP* 3.2 14.3 + - - +
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Residues in contact with ARG 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 3.4 26.7 + - + +
63K LYS 3.0 16.3 + - - +
64K ALA* 3.6 11.1 - - - +
66K GLU* 1.3 77.4 - - - +
68K MET* 1.3 57.9 + - - +
70K ASP* 3.0 8.7 + - - +
71K THR* 2.9 29.5 + - - -
29L GLU* 3.4 32.9 + - - +
66L GLU* 2.9 51.1 + - - +
69L LYS* 3.5 36.8 + - - +
70L ASP* 2.7 28.6 + - - +
73L ARG* 3.6 11.4 + - - +
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Residues in contact with MET 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50K VAL* 3.9 18.4 - - + -
64K ALA 2.9 17.6 + - - +
65K ILE* 3.3 4.5 + - - +
67K ARG* 1.3 75.6 - - - +
69K LYS* 1.3 58.4 + - - +
71K THR* 3.2 3.6 + - - -
72K LEU* 2.9 43.0 + - + +
96K ILE* 4.1 12.3 - - + -
97K ALA 4.4 1.1 - - - +
98K ALA* 4.2 7.2 - - - -
99K ILE* 3.8 28.3 - - + +
29L GLU* 3.6 45.1 + - + +
31L LEU* 3.6 32.3 - - + +
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Residues in contact with LYS 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64J ALA* 6.2 2.0 - - - +
67J ARG* 3.4 30.8 - - - +
27K TYR* 3.8 11.8 + - - +
36K GLU* 4.1 20.2 + - - +
37K MET* 4.5 5.1 - - - +
38K ALA* 3.9 31.0 - - + +
50K VAL* 4.0 13.9 - - + -
51K GLU 5.4 0.2 + - - -
53K PRO* 4.9 3.6 - - - +
65K ILE* 3.1 27.7 + - - +
66K GLU* 2.8 39.9 + - - +
67K ARG 3.2 0.2 - - - -
68K MET* 1.3 76.6 - - - +
70K ASP* 1.3 60.6 + - - +
72K LEU* 3.4 8.7 + - - +
73K ARG* 3.1 22.5 + - - +
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Residues in contact with ASP 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE* 4.1 18.0 - - + +
232B THR* 4.4 13.2 + - - +
235B ARG* 6.1 1.2 - - - +
67J ARG* 2.7 34.3 + - - +
70J ASP* 5.5 1.2 - - - +
66K GLU 3.2 12.0 + - - +
67K ARG* 3.0 10.5 + - - +
69K LYS* 1.3 75.7 - - - +
71K THR* 1.3 58.6 + - - +
73K ARG* 3.1 25.1 + - - +
74K ILE* 2.8 36.9 + - + +
73L ARG* 3.8 15.3 - - - +
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Residues in contact with THR 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67K ARG 2.9 6.3 + - - -
68K MET* 3.2 8.9 + - - -
70K ASP* 1.3 77.0 - - - +
72K LEU* 1.3 58.0 + - - +
74K ILE* 3.4 2.3 + - - +
75K ALA* 2.8 31.8 + - + +
99K ILE* 4.3 25.1 - - + -
101K MET* 4.5 16.2 - - + -
27L TYR* 5.0 1.3 - - + -
29L GLU* 2.7 33.5 + - - +
73L ARG* 2.8 37.4 + - + +
77L LEU* 6.0 0.2 - - - +
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Residues in contact with LEU 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K ILE* 3.7 7.8 - - + +
27K TYR* 4.1 13.8 - - + -
38K ALA* 5.0 5.6 - - + -
40K ILE* 4.1 31.9 - - + +
50K VAL* 3.6 30.7 - - + -
68K MET* 2.9 28.4 + - + +
69K LYS* 3.8 6.3 - - - +
70K ASP 3.2 0.2 - - - -
71K THR* 1.3 73.0 - - - +
73K ARG* 1.3 61.1 + - - +
75K ALA* 4.4 2.2 - - - -
76K TYR* 2.8 31.5 + - - +
85K LEU* 5.3 0.2 - - + -
96K ILE* 3.8 17.9 - - + -
99K ILE* 3.9 27.4 - - + -
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Residues in contact with ARG 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLN* 4.7 5.3 - - - +
230B ILE* 4.2 21.0 - - - +
67J ARG* 3.7 27.9 + - - +
70J ASP* 3.8 22.7 + - - +
71J THR* 2.9 43.6 + - - +
74J ILE* 4.1 15.3 - - - +
101J MET* 4.8 3.8 - - + -
27K TYR* 3.8 26.8 - - + +
29K GLU* 4.2 0.6 + - - -
69K LYS 3.1 14.5 + - - +
70K ASP* 3.6 28.9 + - - +
72K LEU* 1.3 76.4 - - - +
74K ILE* 1.3 64.3 + - - +
76K TYR* 3.3 3.9 + - - +
77K LEU* 3.0 35.7 + - + +
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Residues in contact with ILE 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLN* 3.4 38.4 - - + +
230B ILE* 3.8 22.7 - - + -
70K ASP 2.8 23.0 + - - +
71K THR* 3.7 4.0 - - - +
73K ARG* 1.3 78.6 - - + +
75K ALA* 1.3 60.8 + - - +
77K LEU* 3.2 1.9 + - - +
78K THR* 2.8 32.0 + - + +
73L ARG* 3.6 36.6 - - - +
74L ILE* 4.3 10.3 - - + -
77L LEU* 3.4 31.0 - - + -
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Residues in contact with ALA 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K ILE* 3.9 16.8 + - + +
71K THR 2.8 22.6 + - - +
72K LEU* 3.8 4.5 - - - +
74K ILE* 1.3 74.3 - - - +
76K TYR* 1.3 63.3 + - - +
78K THR* 3.2 6.6 + - - -
79K GLU* 3.2 3.8 + - - -
80K ALA* 3.1 35.2 + - + +
82K VAL* 5.4 1.1 - - + -
99K ILE* 5.3 6.5 - - + -
101K MET* 4.2 23.1 - - + -
77L LEU* 5.3 1.3 - - - -
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Residues in contact with TYR 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J ALA* 5.3 3.4 - - + -
81J LYS 4.8 1.9 + - - -
101J MET* 3.7 28.6 - - + +
102J ALA* 3.1 27.2 + - - -
103J ASN* 3.2 15.1 + - + +
24K ILE* 3.6 41.4 - - + +
25K PHE 3.5 21.3 - - - -
26K SER* 4.0 3.1 - - - -
27K TYR* 3.8 22.7 - - + -
72K LEU 2.8 19.4 + - - +
73K ARG 3.6 3.4 - - - +
75K ALA* 1.3 76.7 - - - +
77K LEU* 1.3 86.3 + - + +
79K GLU* 3.3 17.7 + - - +
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Residues in contact with LEU 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LYS* 4.2 8.8 - - - +
223B PHE* 3.5 23.9 - - + -
227B GLN* 3.7 28.3 - - - +
74J ILE* 3.7 32.3 - - + -
75J ALA* 4.9 1.6 - - - +
78J THR* 4.0 11.0 - - + +
80J ALA* 3.7 29.8 - - + -
101J MET* 4.4 9.2 - - + -
73K ARG* 3.0 25.7 + - + +
74K ILE 3.2 3.1 + - - +
76K TYR* 1.3 96.2 - - + +
78K THR* 1.3 59.6 + - - +
79K GLU* 3.3 1.3 + - - +
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Residues in contact with THR 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B SER 3.6 1.0 - - - +
219B LYS* 4.2 4.3 - - - -
220B ARG* 3.3 37.7 + - - +
223B PHE* 4.0 3.1 - - + -
224B SER* 3.1 38.8 - - - +
227B GLN* 3.7 12.6 - - - +
74K ILE* 2.8 25.2 + - + +
75K ALA* 3.2 11.4 + - - -
77K LEU* 1.3 76.3 - - - +
79K GLU* 1.3 67.7 + - - +
80K ALA* 3.2 11.3 + - - +
77L LEU* 4.3 3.7 - - - +
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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