Contacts of the strand formed by residues 72 - 82 (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 LEU 72 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C LEU* 4.1 8.1 - - + +
15C PRO* 3.7 24.7 - - + -
51C ILE* 4.2 7.4 - - + -
74D PRO* 4.1 26.0 - - + -
162D LEU* 4.9 4.5 - - + -
5E ILE 4.7 1.5 + - - +
6E ASN* 3.5 38.8 - - + +
7E PRO* 3.6 17.1 - - + +
47E ASN* 3.6 27.1 - - + +
49E ILE* 3.6 20.9 - - + -
70F GLY 4.4 2.0 - - - +
71F ALA* 1.3 70.0 - - - +
73F VAL* 1.3 58.9 + - - +
74F PRO* 3.6 6.9 - - - +
163F TRP* 3.6 14.0 - - - -
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Residues in contact with VAL 73 (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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43E ILE* 4.6 4.7 - - + -
46E VAL* 3.9 22.9 - - + -
47E ASN 2.8 12.0 + - - +
48E LEU* 3.5 1.5 - - + -
49E ILE* 2.9 22.4 + - - +
67F LEU* 4.0 13.2 - - + -
71F ALA* 3.9 16.4 - - + +
72F LEU* 1.3 75.1 - - - +
74F PRO* 1.3 63.1 - - - +
75F THR* 2.9 27.5 + - - +
161F ALA* 3.9 15.9 - - + -
162F LEU 3.7 16.4 - - - +
163F TRP* 3.9 18.4 - - + -
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Residues in contact with PRO 74 (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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49A ILE* 5.4 0.9 - - + -
72B LEU* 3.6 32.1 - - + -
7E PRO* 4.1 14.8 - - + -
15E PRO* 4.5 6.5 - - + -
49E ILE* 3.4 17.5 - - + +
51E ILE* 4.0 18.2 - - + -
72F LEU 3.6 8.1 - - - +
73F VAL* 1.3 79.8 - - - +
75F THR* 1.3 60.2 + - - +
162F LEU* 2.9 55.8 + - + +
163F TRP* 4.6 3.1 - - + -
164F TYR* 5.6 0.2 - - + -
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Residues in contact with THR 75 (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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43E ILE* 5.0 0.7 - - + -
48E LEU* 3.4 30.7 - - + +
49E ILE 2.8 11.0 + - - -
50E ARG* 3.3 10.7 - - - +
51E ILE* 3.0 26.0 + - - +
73F VAL* 2.9 22.9 + - - +
74F PRO* 1.3 75.4 + - - +
76F ALA* 1.3 71.7 + - - +
77F TYR* 4.0 9.8 - - + -
159F ALA* 3.6 19.7 - - + -
160F ALA 3.4 14.6 - - - +
161F ALA* 4.1 5.0 - - + +
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Residues in contact with ALA 76 (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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51E ILE* 3.5 28.3 - - + +
53F PYR 4.1 9.6 - - + +
75F THR* 1.3 71.7 - - - +
77F TYR* 1.3 63.0 + - - +
93F ILE* 3.7 4.4 - - + +
107F ILE* 3.7 28.5 - - + -
109F GLU* 4.6 7.4 - - - +
159F ALA* 3.2 1.9 - - - +
160F ALA* 2.8 34.8 + - + +
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Residues in contact with TYR 77 (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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52C SER* 2.6 35.0 + - - -
34E PHE* 4.0 13.2 - + - -
48E LEU* 4.1 16.6 - - + -
50E ARG* 2.8 69.4 + - + +
75F THR* 4.0 20.0 - - + -
76F ALA* 1.3 75.1 - - - +
78F GLY* 1.3 61.3 + - - +
79F TYR* 3.8 22.9 - + - -
93F ILE* 4.1 2.5 - - - -
109F GLU* 3.5 18.8 + - - +
157F PHE* 3.6 22.0 - + + -
158F ALA 3.3 13.0 - - - +
159F ALA* 3.7 4.5 - - + -
7005F MRD 3.4 9.4 - - - +
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Residues in contact with GLY 78 (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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50E ARG* 4.5 1.8 - - - -
77F TYR* 1.3 75.6 - - - +
79F TYR* 1.3 64.2 + - - +
91F ALA* 3.7 7.8 - - - +
92F ALA 5.2 0.9 - - - -
109F GLU* 3.8 13.9 - - - +
110F TYR 4.5 4.3 - - - -
111F GLU* 3.3 17.0 - - - -
157F PHE* 3.5 2.3 - - - -
158F ALA 3.0 31.4 + - - +
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Residues in contact with TYR 79 (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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34E PHE* 3.8 23.8 - + + -
50E ARG* 4.0 23.5 + - - +
77F TYR* 3.8 16.8 - + - -
78F GLY* 1.3 74.9 - - - +
80F ILE* 1.3 65.2 + - - +
81F ILE* 3.8 26.2 - - + -
91F ALA* 4.4 0.4 - - - -
111F GLU* 3.1 25.5 + - - +
155F CYS* 4.4 2.0 - - - -
156F ALA 3.1 13.7 - - - +
157F PHE* 4.1 7.2 - - + -
7005F MRD 3.1 43.4 + - + +
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Residues in contact with ILE 80 (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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79F TYR* 1.3 80.6 - - - +
81F ILE* 1.3 74.0 + - - +
82F SER* 5.6 0.4 - - - -
89F ILE* 3.5 31.8 - - + +
90F SER 3.5 23.6 - - - +
111F GLU* 3.9 8.1 - - + -
112F GLY* 3.7 31.0 - - - +
113F LYS* 4.1 15.3 - - + +
155F CYS* 3.2 4.2 - - - -
156F ALA* 3.0 36.0 + - + +
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Residues in contact with ILE 81 (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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30E PRO* 3.5 40.4 - - + +
33E ALA* 5.0 0.7 - - + -
34E PHE* 4.4 3.8 - - + -
79F TYR* 3.8 19.0 - - + -
80F ILE* 1.3 85.3 - - - +
82F SER* 1.3 62.4 + - - +
153F LEU* 3.8 23.3 - - + -
154F GLY 3.2 11.7 - - - +
155F CYS* 3.8 13.0 - - + -
7005F MRD 3.6 25.6 - - + +
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Residues in contact with SER 82 (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* 5.3 1.6 - - - -
81F ILE* 1.3 76.4 - - - +
83F ASP* 1.3 61.5 + - - +
84F VAL* 3.2 14.1 + - - +
87F GLU* 2.7 28.9 + - - -
89F ILE* 3.8 13.9 - - - +
113F LYS* 5.8 1.6 - - - -
150F VAL* 3.6 18.9 - - - +
153F LEU* 3.4 5.8 - - - +
154F GLY 2.9 32.0 + - - -
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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