Contacts of the helix formed by residues 76 - 92 (chain W) in PDB entry 5IY6
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 THR 76 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74W SER* 3.6 1.1 + - - -
75W ARG* 1.4 100.9 - - + +
77W VAL* 1.3 64.5 + - - +
78W PRO* 3.6 4.8 - - - +
79W GLU* 3.5 17.3 + - - +
80W ILE* 3.5 24.8 + - - +
606W GLU* 2.7 35.0 + - + +
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Residues in contact with VAL 77 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76W THR* 1.3 76.3 - - - +
78W PRO* 1.4 67.1 - - + +
80W ILE* 3.2 18.3 + - - +
81W GLU* 3.5 9.7 + - - +
110W SER* 4.0 25.1 - - - +
114W ASN* 4.2 22.4 - - + +
176W ASN* 5.3 0.3 - - - +
177W LEU* 4.2 26.4 - - + +
178W ASP* 4.9 11.0 - - + +
181W LYS* 5.7 2.7 - - - +
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Residues in contact with PRO 78 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76W THR* 3.6 9.4 - - - +
77W VAL* 1.4 91.7 - - + +
79W GLU* 1.3 60.1 + - + +
81W GLU* 3.3 17.4 + - + +
82W LYS* 3.4 19.1 + - + +
606W GLU* 3.5 31.2 - - + +
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Residues in contact with GLU 79 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74W SER* 5.3 7.2 - - - -
75W ARG* 4.3 26.7 + - - +
76W THR* 3.5 23.6 + - - +
77W VAL 3.4 0.8 - - - -
78W PRO* 1.3 75.0 - - + +
80W ILE* 1.3 65.1 + - - +
82W LYS* 3.1 30.5 + - + +
83W VAL* 3.1 24.7 + - + +
606W GLU* 4.7 22.1 - - + +
666W ARG* 4.8 12.3 + - - -
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Residues in contact with ILE 80 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74W SER* 3.4 26.0 - - - +
76W THR 3.5 15.0 + - - +
77W VAL* 3.2 16.2 + - + +
79W GLU* 1.3 77.7 - - - +
81W GLU* 1.3 62.8 + - - +
83W VAL* 3.1 10.6 + - - +
84W ILE* 3.0 20.6 + - + +
108W ALA* 3.9 19.3 - - + -
109W LEU 3.6 10.5 - - - +
110W SER* 3.3 26.5 - - - +
176W ASN* 4.9 2.7 - - - +
177W LEU* 5.0 7.6 - - + -
206W VAL* 3.6 30.1 - - + +
207W TYR* 5.1 2.0 - - - -
208W SER* 6.2 0.4 - - - -
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Residues in contact with GLU 81 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77W VAL 3.5 6.4 + - - +
78W PRO* 3.3 12.3 + - + +
80W ILE* 1.3 77.3 - - - +
82W LYS* 1.3 52.7 + - + +
84W ILE* 3.3 2.0 + - - +
85W GLU* 2.8 63.2 + - + +
176W ASN* 2.8 44.4 + - - +
178W ASP* 4.2 10.2 - - - +
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Residues in contact with LYS 82 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78W PRO* 3.5 16.6 - - + +
79W GLU* 3.1 29.6 + - + +
81W GLU* 1.3 76.8 - - + +
83W VAL* 1.4 59.5 + - - +
85W GLU* 4.6 3.8 - - - +
86W GLU* 3.4 31.5 + - + +
606W GLU 5.4 3.2 + - - -
608W ILE 5.8 0.8 - - - -
609W ASP* 3.5 47.5 + - + +
666W ARG* 3.7 28.5 - - - +
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Residues in contact with VAL 83 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49W THR* 4.3 29.6 - - + +
72W TYR* 5.3 12.3 - - + -
74W SER* 5.5 4.7 - - - -
79W GLU* 3.1 16.3 + - + +
80W ILE* 3.1 8.5 + - - +
82W LYS* 1.4 76.2 - - - +
84W ILE* 1.3 52.9 + - - +
86W GLU* 3.8 2.4 - - - +
87W LEU* 2.9 50.6 + - + +
206W VAL* 4.2 33.2 - - + -
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Residues in contact with ILE 84 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80W ILE* 3.0 21.9 + - + +
81W GLU* 3.8 6.3 - - - +
83W VAL* 1.3 73.3 - - - +
85W GLU* 1.3 59.1 + - + +
87W LEU* 3.9 15.9 - - + +
88W ARG* 2.8 68.2 + - + +
107W LEU* 4.1 8.5 - - - +
108W ALA* 3.7 7.6 - - + +
174W ILE* 3.6 11.2 - - + +
175W TYR 3.4 24.5 - - - +
176W ASN* 4.1 8.1 - - + +
206W VAL* 3.6 27.4 - - + -
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Residues in contact with GLU 85 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81W GLU* 2.8 48.1 + - + +
82W LYS* 4.6 3.8 - - - +
84W ILE* 1.3 71.0 - - + +
86W GLU* 1.3 64.5 + - + +
88W ARG* 2.8 38.8 + - - +
89W LYS* 3.1 39.6 + - - +
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Residues in contact with GLU 86 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46W THR* 6.2 0.2 - - - -
47W GLY 5.4 5.9 + - - -
49W THR* 4.4 12.4 + - + +
50W VAL* 3.8 44.5 + - + +
82W LYS* 3.4 21.5 + - - +
83W VAL* 3.8 3.4 - - - +
84W ILE 3.4 0.2 - - - -
85W GLU* 1.3 78.0 - - + +
87W LEU* 1.4 63.2 + - - +
89W LYS* 3.2 20.6 + - - +
90W LEU* 3.0 22.6 + - - +
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Residues in contact with LEU 87 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53W LEU* 3.7 35.7 - - + -
72W TYR* 5.9 2.5 - - + -
83W VAL* 2.9 34.9 + - + +
84W ILE* 4.2 14.6 - - + +
86W GLU* 1.4 72.3 - - - +
88W ARG* 1.3 58.2 + - - +
90W LEU* 3.3 1.4 + - - -
91W LEU* 2.9 47.6 + - + +
106W GLY* 4.8 6.7 - - - -
174W ILE* 3.7 26.9 - - + -
204W VAL* 3.8 31.6 - - + -
206W VAL* 6.1 1.6 - - + -
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Residues in contact with ARG 88 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81W GLU* 6.1 0.2 - - - +
84W ILE* 2.8 36.0 + - - +
85W GLU* 2.8 41.4 + - - +
87W LEU* 1.3 72.2 - - - +
89W LYS* 1.3 56.7 + - + +
91W LEU* 4.1 3.9 - - - +
92W ASN* 2.9 30.3 + - - -
173W GLY 3.5 12.2 + - - +
174W ILE* 2.8 49.2 + - + -
175W TYR* 4.1 1.2 - - - +
176W ASN* 3.5 26.0 - - - +
179W ASP* 5.7 4.0 + - - +
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Residues in contact with LYS 89 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85W GLU* 3.1 31.8 + - - +
86W GLU* 3.2 18.1 + - - +
88W ARG* 1.3 73.7 - - + +
90W LEU* 1.3 62.7 + - - +
92W ASN* 3.7 16.3 + - - +
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Residues in contact with LEU 90 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17W ILE* 4.4 16.6 - - + -
18W TYR* 3.7 23.8 - - + +
50W VAL* 4.3 10.1 - - + +
53W LEU* 3.5 52.0 - - + +
54W ALA* 4.0 4.3 - - + +
57W MET* 5.7 1.3 - - - -
86W GLU 3.0 12.7 + - - +
87W LEU 3.3 7.4 + - - +
89W LYS* 1.3 76.6 - - - +
91W LEU* 1.3 60.6 + - - +
92W ASN* 4.6 1.4 - - - +
100W GLU 5.4 0.3 + - - -
101W LYS* 4.1 29.7 + - + +
102W LEU* 4.3 9.9 - - + -
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Residues in contact with LEU 91 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53W LEU* 4.0 12.3 - - + -
87W LEU* 2.9 39.5 + - + +
88W ARG* 4.1 3.4 - - - +
90W LEU* 1.3 70.5 - - - +
92W ASN* 1.3 62.8 + - - +
93W PHE* 2.8 28.8 + - - +
99W GLY* 3.4 11.8 - - - -
100W GLU 4.0 4.0 + - - -
102W LEU* 3.8 47.7 - - + +
104W PHE* 3.3 37.5 - - + +
105W LEU* 4.4 1.1 - - - +
106W GLY 5.0 1.8 - - - +
174W ILE* 4.7 17.7 - - + -
204W VAL* 6.0 1.3 - - + -
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Residues in contact with ASN 92 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88W ARG 2.9 19.3 + - - -
89W LYS* 3.7 13.4 + - - +
90W LEU 3.5 1.9 - - - +
91W LEU* 1.3 78.0 - - - +
93W PHE* 1.4 61.9 + - - +
98W GLU* 2.9 35.2 + - - +
99W GLY* 4.6 1.3 - - - -
100W GLU 5.3 1.1 - - - +
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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
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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