Contacts of the strand formed by residues 78 - 85 (chain F) in PDB entry 3N2N
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 78 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43F PHE* 3.7 32.5 - - + -
45F LEU* 3.7 24.7 - - + -
69F LEU 5.5 0.7 - - - +
73F PHE* 3.6 32.1 - - + +
75F SER* 3.0 9.5 + - - +
76F PRO 3.8 2.0 - - - +
77F GLN* 1.3 77.1 - - - +
79F ARG* 1.3 76.0 + - - +
80F MET* 3.8 22.4 - - + -
97F GLU* 4.2 0.2 - - - -
99F ARG* 2.8 33.5 + - - +
212F ILE* 4.3 10.3 - - + -
216F LEU* 4.2 14.8 - - + +
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Residues in contact with ARG 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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42F GLY* 6.2 1.0 - - - -
43F PHE 2.9 8.2 + - - +
44F ASP* 2.9 39.9 + - - +
45F LEU* 2.8 27.7 + - - +
76F PRO 4.4 3.1 - - - +
77F GLN 5.0 2.7 - - - +
78F LEU* 1.3 75.8 - - - +
80F MET* 1.3 63.3 + - - +
95F LEU* 3.7 19.4 + - + +
96F THR* 3.2 11.9 - - - +
97F GLU* 3.6 39.0 - - + +
134F GLU* 2.7 34.3 + - - +
141F THR* 5.7 0.8 + - - +
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Residues in contact with MET 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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45F LEU* 3.1 18.2 - - + +
47F PHE* 4.3 14.6 - - + -
70F ALA* 4.0 30.5 - - + +
73F PHE 4.2 0.7 - - - +
78F LEU* 3.8 19.7 - - + -
79F ARG* 1.3 75.6 - - - +
81F SER* 1.3 60.0 + - - +
82F PHE* 3.8 24.2 - - + -
93F MET* 3.2 19.0 - - + +
95F LEU* 3.4 4.6 - - - -
96F THR 3.0 26.6 + - - +
99F ARG* 3.6 27.6 - - - +
102F ILE* 3.9 25.1 - - + -
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Residues in contact with SER 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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45F LEU 2.9 5.7 + - - +
46F TYR* 3.8 24.9 - - - -
47F PHE* 3.0 26.6 + - - +
80F MET* 1.3 74.8 - - - +
82F PHE* 1.3 68.2 + - - +
83F ILE* 4.0 4.5 - - - +
91F THR* 3.9 2.6 - - - +
93F MET* 2.7 22.2 + - - -
95F LEU* 3.6 14.8 - - - -
130F GLN* 3.0 21.3 + - - -
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Residues in contact with PHE 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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47F PHE* 3.7 21.1 - + + -
49F LEU* 5.1 1.1 - - + -
66F VAL* 3.6 18.6 - - + -
80F MET* 3.8 27.1 - - + -
81F SER* 1.3 78.1 - - - +
83F ILE* 1.3 63.5 + - - +
91F THR 3.7 0.7 - - - -
92F LEU* 2.8 39.5 + - + -
93F MET* 2.9 44.4 + - + +
102F ILE* 4.0 6.3 - - + -
105F GLY* 3.9 9.6 - - - -
106F LEU* 3.7 42.6 - - + -
109F LEU* 3.7 24.9 - - + -
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Residues in contact with ILE 83 (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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46F TYR* 4.6 7.0 - - + -
47F PHE 2.8 16.9 + - - +
48F ILE* 4.2 11.2 - - + -
49F LEU* 2.7 36.4 + - - +
81F SER* 4.0 9.0 - - - +
82F PHE* 1.3 79.0 - - - +
84F VAL* 1.3 63.4 + - - +
90F THR 3.5 11.4 - - - +
91F THR* 4.1 8.1 - - - +
123F GLY* 3.7 28.5 - - - +
126F ARG* 3.8 17.0 - - + -
127F ALA* 3.5 41.1 - - + +
130F GLN* 3.9 8.5 - - - +
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Residues in contact with VAL 84 (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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49F LEU* 3.4 5.4 - - + +
51F LYS* 3.9 22.4 - - + +
59F TRP* 4.4 13.9 - - + -
83F ILE* 1.3 81.4 - - - +
85F PHE* 1.3 64.1 + - - +
88F ARG 4.0 0.3 - - - +
89F GLY* 3.5 0.3 - - - -
90F THR* 2.9 49.3 + - - +
92F LEU* 4.2 15.3 - - + -
109F LEU* 3.8 29.4 - - + -
112F VAL* 4.6 5.6 - - + -
224F ACT 3.7 21.3 - - - +
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Residues in contact with PHE 85 (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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48F ILE* 3.6 33.0 - - + -
49F LEU 2.9 22.5 + - - -
50F ASP* 3.4 38.6 - - + -
51F LYS* 2.8 29.9 + - - +
52F SER 3.8 0.5 + - - -
84F VAL* 1.3 77.7 - - - +
86F SER* 1.3 63.0 + - - +
88F ARG 3.2 10.1 - - - +
89F GLY* 3.9 8.5 - - - -
118F THR* 3.6 20.4 - - + -
119F TYR 3.9 13.2 - - - +
120F MET* 3.5 53.4 - - + -
123F GLY* 4.3 4.5 - - - +
147F ALA* 5.9 0.2 - - + -
148F LEU 4.4 0.9 - - - -
149F THR* 4.3 2.0 - - - -
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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