Contacts of the strand formed by residues 88 - 98 (chain F) in PDB entry 1N13
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 88 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86F GLY 3.6 6.2 + - - -
87F GLU* 1.3 76.2 - - - +
89F ILE* 1.3 66.8 + - - +
113F LYS* 3.5 20.1 - - - +
114F CYS* 3.6 22.2 + - - +
115F SER* 4.6 2.2 - - - -
147F GLU* 4.0 22.7 - - + +
148F HIS 3.3 9.4 - - - +
149F THR* 3.9 16.5 + - - +
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Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ILE* 3.5 41.5 - - + +
82F SER* 3.8 27.1 - - - +
87F GLU* 4.2 12.6 - - + +
88F THR* 1.3 76.9 - - - +
90F SER* 1.3 65.6 + - - +
112F GLY 3.5 4.3 - - - +
113F LYS* 4.4 3.4 - - + -
147F GLU* 3.2 0.3 - - - +
148F HIS* 2.7 46.4 + - + +
150F VAL* 4.1 8.3 - - + -
154F GLY 3.5 29.2 - - - +
155F CYS 4.2 0.4 - - - -
156F ALA* 3.8 15.7 - - + +
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Residues in contact with SER 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ILE* 3.5 5.4 - - - +
89F ILE* 1.3 71.9 + - - +
91F ALA* 1.3 60.0 + - - +
111F GLU* 3.2 3.0 - - - -
112F GLY 2.9 33.0 + - - -
114F CYS* 2.7 24.6 + - - -
115F SER 3.2 17.0 - - - -
116F LYS* 4.1 1.1 - - - -
119F ALA* 3.8 12.8 - - - -
146F VAL 3.1 10.5 - - - -
147F GLU* 3.1 22.9 - - - +
156F ALA* 3.9 5.4 - - - -
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Residues in contact with ALA 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F GLY 3.7 20.0 - - - +
79F TYR* 4.4 1.6 - - - -
90F SER* 1.3 76.0 - - - +
92F ALA* 1.3 62.2 + - - +
110F TYR 3.2 9.9 - - - +
111F GLU* 4.4 0.9 - - + -
119F ALA* 4.6 1.8 - - - -
145F ALA* 3.3 2.3 - - - +
146F VAL* 2.9 30.2 + - + +
156F ALA* 3.6 27.6 - - + +
157F PHE 3.8 1.1 - - - +
158F ALA* 3.7 14.9 - - - +
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Residues in contact with ALA 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F GLY* 5.2 0.5 - - - -
91F ALA* 1.3 77.1 - - - +
93F ILE* 1.3 64.8 + - - +
109F GLU* 3.4 3.5 - - - +
110F TYR* 2.8 33.8 + - + +
119F ALA* 3.7 29.6 - - + +
120F GLU* 3.9 0.4 - - - +
123F VAL* 3.7 12.8 - - + -
144F ILE 3.2 14.4 - - - +
145F ALA* 3.6 12.1 - - + -
158F ALA* 3.6 3.2 - - - +
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Residues in contact with ILE 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E LEU* 3.6 29.4 - - + -
76F ALA* 3.7 22.4 - - + +
77F TYR* 4.1 0.2 - - - -
92F ALA* 1.3 75.5 - - - +
94F SER* 1.3 68.3 + - - +
107F ILE* 4.3 6.3 - - + -
108F MET 3.4 7.9 - - - +
109F GLU* 3.5 27.6 - - + -
123F VAL* 3.9 3.1 - - - +
143F SER* 3.2 5.7 - - - -
144F ILE* 2.9 41.1 + - + +
158F ALA 3.3 29.6 - - - +
159F ALA 3.5 3.4 - - - +
160F ALA* 3.9 10.5 - - + +
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Residues in contact with SER 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ILE* 1.3 76.2 - - - +
95F VAL* 1.3 66.5 + - - +
96F ALA 4.2 0.2 - - - -
106F LEU 4.3 0.2 - - - -
107F ILE* 3.2 5.7 - - - +
108F MET* 2.9 38.0 + - - +
123F VAL* 2.7 37.8 + - - +
124F ARG* 4.1 0.9 - - - -
127F ALA* 3.3 10.3 - - - +
141F ILE* 3.8 18.8 - - - -
142F GLU 3.3 5.8 - - - -
143F SER* 4.1 2.2 - - - -
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Residues in contact with VAL 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E VAL* 4.5 8.5 - - + -
20E LEU* 3.6 30.5 - - + -
55F MET* 4.0 29.6 - - + -
61F ILE* 4.2 13.2 - - + -
94F SER* 1.3 80.2 - - - +
96F ALA* 1.3 70.3 + - - +
97F ILE* 3.5 6.1 + - + +
106F LEU 3.3 7.6 - - - +
107F ILE* 4.1 23.3 - - + -
140F ARG 3.9 0.2 - - - +
141F ILE* 3.4 4.1 - - - -
142F GLU* 2.8 33.3 + - + +
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Residues in contact with ALA 96 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94F SER 4.2 0.6 - - - -
95F VAL* 1.3 70.9 - - - +
97F ILE* 1.3 60.8 + - - +
105F GLY* 3.1 8.5 - - - -
106F LEU* 2.7 37.3 + - + +
127F ALA* 3.8 23.6 - - + +
131F PHE* 3.5 22.1 - - + -
138F LEU* 3.5 18.6 - - + -
140F ARG 3.7 5.2 - - - -
141F ILE* 4.2 4.9 - - + -
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Residues in contact with ILE 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F MET* 4.3 17.5 - - + -
61F ILE* 3.9 13.5 - - + -
95F VAL* 3.9 12.8 - - + +
96F ALA* 1.3 76.3 - - - +
98F PRO* 1.3 68.2 - - + +
101F LYS* 3.5 16.6 - - + +
131F PHE* 4.1 2.0 - - - -
138F LEU* 3.5 3.6 - - - +
139F ASP* 2.8 43.3 + - - +
140F ARG* 2.9 47.5 + - + +
142F GLU* 3.6 23.1 - - + -
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Residues in contact with PRO 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F MET* 4.3 5.6 - - + -
97F ILE* 1.3 90.3 - - + +
99F LYS* 1.3 62.5 + - - +
100F ASP 3.4 23.3 - - - +
101F LYS* 2.9 29.3 + - + -
103F LEU* 3.5 20.2 - - + +
104F CYS 3.5 23.8 - - - +
105F GLY* 4.0 8.5 - - - -
131F PHE* 3.6 18.1 - - + -
137F GLU 3.5 9.4 - - - +
139F ASP* 3.6 1.9 - - - +
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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
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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