Contacts of the helix formed by residues 87 - 104 (chain I) in PDB entry 4DHJ
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 ASN 87 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I ASP* 2.9 10.9 + - - +
86I GLY* 1.3 78.1 - - - +
88I CYS* 1.3 65.9 + - - +
89I PHE 3.1 2.9 - - - -
90I TYR* 2.9 18.7 + - - +
91I ARG* 3.0 23.1 + - - +
170I LEU* 3.7 20.6 - - + -
174I ARG* 2.8 33.9 + - - +
209I MET* 3.5 20.7 - - - +
210I TRP* 3.0 43.9 + - - -
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Residues in contact with CYS 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I ILE* 3.8 12.7 - - + +
83I ARG 3.7 13.9 - - - +
85I ASP* 3.6 2.6 + - - -
87I ASN* 1.3 75.6 - - - +
89I PHE* 1.3 65.9 + - - +
91I ARG* 3.8 0.2 - - - +
92I ALA* 2.8 34.6 + - - +
267I HIS* 3.8 3.1 - - + -
268I TYR* 3.5 35.7 - - - +
575J GLY 3.7 2.9 - - - -
576J GLZ 1.8 69.8 - - - +
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Residues in contact with PHE 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I GLY 5.3 0.2 + - - -
87I ASN 3.0 1.2 + - - -
88I CYS* 1.3 83.1 - - - +
90I TYR* 1.3 71.6 + + + +
92I ALA* 3.7 1.5 - - - +
93I ILE* 3.0 47.0 + - + +
213I ALA* 3.7 32.3 - - + +
217I ALA 4.5 0.9 - - - -
218I ILE* 3.6 55.0 - - + -
221I LEU* 3.8 23.8 - - + -
222I ILE* 4.1 6.1 - - + -
231I ILE* 5.2 1.3 - - + -
261I LEU* 3.8 21.3 - - + -
268I TYR* 3.9 28.7 - + + -
575J GLY 4.5 3.5 + - - +
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Residues in contact with TYR 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I GLY 4.9 0.4 - - - -
87I ASN* 2.9 13.9 + - - +
89I PHE* 1.3 80.2 - + + +
91I ARG* 1.3 59.1 + - - +
93I ILE* 3.6 2.1 + - - +
94I LEU* 2.9 32.6 + - - +
170I LEU* 4.0 18.2 - - + -
173I PHE* 4.3 10.1 - - + +
174I ARG* 3.4 59.4 + - + -
177I THR* 3.6 24.2 - - + -
205I GLU 4.7 1.0 + - - -
206I ILE* 3.9 12.6 - - - +
211I LYS 4.0 3.6 - - - -
213I ALA* 3.7 23.9 - - + +
217I ALA* 3.6 22.4 - - + +
221I LEU* 3.8 25.0 - - + +
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Residues in contact with ARG 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I LEU* 3.5 45.9 + - - +
44I VAL* 3.9 17.9 - - + -
82I ILE* 3.8 13.3 - - + +
83I ARG* 5.1 1.4 + - - +
85I ASP* 3.1 28.7 + - - -
87I ASN* 3.0 28.9 + - - +
88I CYS 3.8 2.7 - - - +
90I TYR* 1.3 76.8 - - - +
92I ALA* 1.3 59.5 + - - +
94I LEU* 3.3 13.6 + - + +
95I VAL* 2.9 37.0 + - + +
160I LEU 4.9 0.6 + - - +
166I ALA* 3.9 19.2 + - - +
167I ASN* 2.9 29.5 + - - -
170I LEU* 3.7 18.1 - - + +
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Residues in contact with ALA 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I ILE* 4.2 14.0 - - + +
88I CYS 2.8 23.4 + - - +
89I PHE 3.7 3.6 - - - +
91I ARG* 1.3 72.7 - - - +
93I ILE* 1.3 57.6 + - - +
95I VAL* 3.6 2.4 - - - +
96I GLY* 2.9 25.8 + - - -
261I LEU* 3.7 29.3 - - + +
268I TYR* 4.5 9.2 - - + +
269I ASP 4.8 0.4 - - - -
270I VAL* 3.7 20.9 - - + +
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Residues in contact with ILE 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I PHE* 3.0 45.5 + - + +
90I TYR 3.9 0.7 - - - +
92I ALA* 1.3 74.3 - - - +
94I LEU* 1.3 59.9 + - - +
96I GLY* 3.0 2.6 + - - -
97I LEU* 2.7 48.2 + - + +
173I PHE* 5.3 0.9 - - + -
221I LEU* 3.8 26.5 - - + -
222I ILE* 4.3 3.6 - - + -
225I ALA* 5.2 0.4 - - + -
227I THR* 5.0 6.3 - - + -
229I VAL* 3.8 29.4 - - + -
259I ILE* 4.0 10.6 - - + +
261I LEU* 3.8 20.4 - - + -
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Residues in contact with LEU 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I TYR 2.9 23.1 + - - +
91I ARG* 3.3 16.1 + - + +
93I ILE* 1.3 77.1 - - - +
95I VAL* 1.3 65.8 + - + +
97I LEU* 3.4 2.8 + - - +
98I ILE* 2.9 37.3 + - + +
160I LEU* 3.8 29.6 - - + -
166I ALA 5.0 2.0 - - - +
169I ILE* 4.1 9.4 - - + -
170I LEU* 3.7 31.4 - - + -
173I PHE* 3.5 44.6 - - + -
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Residues in contact with VAL 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I VAL* 3.7 33.2 - - + -
80I ARG* 3.8 32.1 - - - +
82I ILE* 4.4 2.5 - - + -
91I ARG* 2.9 21.0 + - + +
92I ALA* 3.6 5.6 - - - +
94I LEU* 1.3 80.9 - - + +
96I GLY* 1.3 61.8 + - - +
98I ILE* 3.4 5.8 + - - +
99I GLU* 3.0 33.4 + - + +
157I TYR* 4.9 5.6 - - + -
160I LEU* 4.1 16.4 - - + -
270I VAL* 4.6 7.0 - - + -
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Residues in contact with GLY 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I ALA 2.9 17.3 + - - -
93I ILE 3.0 4.5 + - - -
95I VAL* 1.3 72.7 - - - +
97I LEU* 1.3 61.6 + - - +
99I GLU* 3.4 13.0 + - - +
100I ILE* 3.2 25.1 + - - +
259I ILE* 3.7 28.1 - - - +
270I VAL* 5.1 3.3 - - - +
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Residues in contact with LEU 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I ILE* 2.7 31.4 + - + +
94I LEU* 3.8 4.3 - - - +
96I GLY* 1.3 71.7 - - - +
98I ILE* 1.3 64.0 + - + +
100I ILE* 3.2 13.0 + - + +
101I MET* 3.0 37.4 + - + +
107I ARG* 4.8 7.0 - - - +
111I PHE* 3.9 13.9 - - + -
173I PHE* 3.6 26.2 - - + -
225I ALA* 3.5 32.5 - - + +
227I THR* 3.8 30.5 - - + +
259I ILE* 3.7 3.3 - - + +
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Residues in contact with ILE 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I LEU* 2.9 34.0 + - + +
95I VAL* 3.8 6.7 - - - +
97I LEU* 1.3 75.1 - - + +
99I GLU* 1.3 59.2 + - + +
101I MET* 3.2 25.5 + - + +
102I LEU* 2.9 38.5 + - + +
139I PHE* 4.6 8.3 - - + -
142I PHE* 3.9 24.0 - - + -
143I LEU* 4.1 8.1 - - + -
146I ILE* 4.4 8.5 - - + -
156I VAL* 3.8 29.2 - - + -
157I TYR* 6.0 1.1 - - + +
160I LEU* 4.7 11.4 - - + -
169I ILE* 6.2 0.9 - - + -
173I PHE* 5.4 2.2 - - + -
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Residues in contact with GLU 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I LEU* 5.4 0.2 - - - +
80I ARG* 2.6 36.0 + - - -
95I VAL* 3.0 24.2 + - + +
96I GLY* 3.7 11.5 - - - +
98I ILE* 1.3 72.5 - - + +
100I ILE* 1.3 66.1 + - - +
102I LEU* 3.4 16.4 + - + +
103I LYS* 3.4 27.2 + - - +
157I TYR* 3.0 19.1 + - + +
270I VAL* 4.5 1.2 - - - +
272I TYR* 2.6 35.9 + - - -
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Residues in contact with ILE 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I GLY 3.2 14.8 + - - +
97I LEU* 3.2 12.5 + - + +
99I GLU* 1.3 77.5 - - + +
101I MET* 1.3 60.2 + - + +
103I LYS* 3.1 9.6 + - - +
104I ASP* 2.9 28.6 + - + +
107I ARG* 4.2 39.3 - - + +
227I THR* 4.2 2.5 - - - +
258I GLU* 3.4 47.8 - - + +
259I ILE* 4.0 12.8 - - + -
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Residues in contact with MET 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I LEU* 3.0 28.0 + - + +
98I ILE* 3.2 37.4 + - + +
100I ILE* 1.3 77.7 - - + +
102I LEU* 1.3 62.6 + - - +
103I LYS 3.2 0.7 + - - -
104I ASP 3.2 21.6 + - - +
105I ARG* 4.1 1.2 + - - -
107I ARG* 4.3 7.6 - - + -
108I LEU* 3.8 41.6 - - + +
111I PHE* 3.5 51.4 - - + -
143I LEU* 4.1 13.2 - - + -
146I ILE* 5.7 4.0 - - + -
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Residues in contact with LEU 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I ILE* 2.9 38.3 + - + +
99I GLU* 3.9 10.5 - - - +
100I ILE 3.3 0.6 - - - -
101I MET* 1.3 76.8 - - - +
103I LYS* 1.3 62.7 + - + +
146I ILE* 3.8 28.0 - - + -
151I HIS 5.4 0.7 - - - +
152I THR 5.3 0.2 - - - -
153I GLU* 4.0 42.0 - - + +
156I VAL* 4.3 18.4 - - + -
157I TYR* 4.5 13.5 - - + +
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Residues in contact with LYS 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I GLU* 3.4 26.0 + - - +
100I ILE* 3.1 8.2 + - - +
101I MET 3.1 0.4 - - - -
102I LEU* 1.3 82.3 - - + +
104I ASP* 1.3 59.4 + - - +
105I ARG 4.0 1.8 + - - -
153I GLU* 5.9 2.2 - - - +
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Residues in contact with ASP 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100I ILE* 2.9 16.1 + - + +
101I MET* 3.2 10.2 - - - +
103I LYS* 1.3 78.9 - - - +
105I ARG* 1.3 64.3 + - - +
106I ALA* 3.0 22.7 + - - +
107I ARG* 3.3 29.7 + - + +
108I LEU 3.1 17.3 + - - -
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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