Contacts of the strand formed by residues 42 - 50 (chain A) 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 GLY 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TYR* 3.2 11.2 - - - +
41A GLY* 1.3 80.7 - - - +
43A PHE* 1.3 60.2 - - - -
44A ASP* 4.1 2.5 - - - -
77A GLN 5.2 1.6 - - - -
79A ARG* 6.3 0.4 - - - -
139A TYR* 5.7 0.2 - - - -
140A ARG 3.1 5.1 + - - -
141A THR* 3.3 18.2 - - - +
142A ALA 2.9 23.9 + - - -
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Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR* 5.6 0.9 - - + -
42A GLY* 1.3 73.9 - - - +
44A ASP* 1.3 66.3 + - - +
45A LEU* 4.8 4.9 - - + -
77A GLN 3.6 17.3 + - - +
78A LEU* 3.6 25.4 - - + +
79A ARG* 2.8 29.2 + - - +
142A ALA* 3.4 11.4 - - + -
144A VAL* 3.8 27.4 - - + -
212A ILE* 3.7 39.5 - - + -
215A ILE* 3.7 46.2 - - + +
216A LEU* 4.0 20.0 - - + -
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Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLY* 4.8 1.0 - - - -
43A PHE* 1.3 83.4 + - - +
45A LEU* 1.3 60.6 + - - +
46A TYR* 3.7 22.8 + - + -
79A ARG* 2.9 41.5 + - - +
95A LEU* 3.4 18.5 - - + +
134A GLU* 4.2 7.3 - - - +
141A THR* 4.2 19.5 + - - +
142A ALA 2.8 12.0 + - - +
143A SER* 3.5 6.4 + - - +
144A VAL 2.9 27.4 + - - +
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 4.8 5.8 - - + -
44A ASP* 1.3 71.8 - - - +
46A TYR* 1.3 62.1 + - - +
47A PHE* 3.7 33.3 + - + -
69A LEU* 5.3 1.1 - - + -
78A LEU* 3.8 24.7 - - + -
79A ARG 2.8 15.7 + - - +
80A MET* 3.1 9.1 - - + +
81A SER 2.9 25.1 + - - +
95A LEU* 4.2 1.0 - - - +
144A VAL* 3.4 26.7 - - + +
146A ILE* 3.6 28.7 - - + -
212A ILE* 4.0 25.6 - - + -
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Residues in contact with TYR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASP* 3.7 28.8 + - + +
45A LEU* 1.3 72.2 - - - +
47A PHE* 1.3 62.0 + - - +
48A ILE* 3.6 1.5 + - + -
81A SER* 3.8 18.4 - - - -
83A ILE* 4.5 5.6 - - + -
95A LEU* 3.5 27.0 - - + +
127A ALA* 4.2 19.5 - - + -
130A GLN* 3.7 32.7 - - + -
131A ILE* 3.5 41.5 + - + +
134A GLU* 4.0 5.4 - - - +
143A SER* 4.4 6.9 + - - -
144A VAL 2.8 22.0 + - - +
145A ILE* 3.3 15.4 - - + +
146A ILE 2.9 26.1 + - - +
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.7 32.8 - - + -
46A TYR* 1.3 71.6 - - - +
48A ILE* 1.3 59.8 + - - +
49A LEU* 3.9 17.5 - - + -
65A PHE* 4.8 2.7 - + - -
66A VAL* 3.8 30.1 - - + -
69A LEU* 3.9 34.5 - - + -
70A ALA 5.4 0.7 - - - -
80A MET* 4.4 12.3 - - + -
81A SER 2.9 13.6 + - - +
82A PHE* 3.6 34.1 - + + -
83A ILE* 2.8 33.8 + - - +
146A ILE* 3.4 27.4 - - + -
148A LEU* 4.6 0.9 - - + -
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Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TYR 4.3 2.0 - - - +
47A PHE* 1.3 74.8 - - - +
49A LEU* 1.3 59.6 + - - +
50A ASP 4.0 0.2 + - - -
83A ILE* 3.6 14.4 - - + -
85A PHE* 3.6 26.9 - - + -
123A GLY* 3.6 34.1 - - - +
124A PHE* 3.8 32.1 - - + +
127A ALA* 3.9 11.4 - - + -
145A ILE* 3.6 26.7 - - + -
146A ILE 2.8 12.2 + - - +
147A ALA* 3.2 9.0 - - + +
148A LEU 2.9 28.4 + - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 3.9 18.2 - - + +
48A ILE* 1.3 78.9 - - - +
50A ASP* 1.3 61.9 + - - +
51A LYS 3.4 0.5 + - - -
59A TRP* 3.9 20.0 - - + -
62A ILE* 4.0 4.5 - - + -
63A TYR* 6.1 0.4 - - - -
66A VAL* 3.7 28.7 - - + -
82A PHE* 5.1 1.8 - - + -
83A ILE 2.8 18.9 + - - +
84A VAL* 3.4 4.4 - - + +
85A PHE* 2.9 30.7 + - - -
109A LEU* 3.8 39.7 - - + -
148A LEU* 3.8 27.8 - - + -
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Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 1.3 69.6 - - - +
51A LYS* 1.3 58.9 + - - +
52A SER* 2.6 40.9 + - - -
55A VAL* 3.3 21.7 - - + +
59A TRP* 3.2 14.6 - - - -
62A ILE* 3.4 7.1 - - + +
85A PHE* 3.4 23.2 - - + -
118A THR* 3.6 12.2 - - - +
148A LEU* 2.9 22.5 + - - +
149A THR* 2.7 28.3 + - - -
150A ASP* 3.8 7.6 - - - +
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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