Contacts of the strand formed by residues 32 - 40 (chain N) in PDB entry 2A3W
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 32 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30N LEU* 3.4 13.8 - - - +
31N GLN* 1.3 104.6 + - - +
33N PHE* 1.3 67.3 + - - +
98N TRP 3.5 4.5 - - - -
99N GLU* 3.7 21.6 - - - +
100N SER 4.0 0.5 + - - -
101N SER* 5.1 0.9 + - - -
161N ASP 3.2 21.4 + - - +
162N SER* 3.9 15.7 - - - +
163N VAL* 3.9 19.7 - - + +
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Residues in contact with PHE 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N LEU* 4.3 9.0 - - + -
32N ASN* 1.3 78.3 - - - +
34N THR* 1.3 69.4 + - - +
35N LEU* 4.1 4.7 - - + -
61N LEU* 3.5 38.1 - - + -
73N LEU* 4.3 7.4 - - + -
75N ILE* 3.6 18.6 - - + -
96N VAL* 3.8 23.3 - - + -
97N SER* 3.2 4.7 - - - -
98N TRP* 3.1 69.8 + + + +
125N VAL* 4.6 6.3 - - + -
159N MET* 3.9 23.8 - - + -
160N TRP 3.2 13.5 - - - +
162N SER 3.3 9.6 + - - +
163N VAL* 4.5 0.3 - - - -
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Residues in contact with THR 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N PHE* 1.3 76.8 + - - +
35N LEU* 1.3 62.1 + - - +
36N CYS* 4.1 8.3 - - - -
96N VAL 3.5 9.2 - - - +
97N SER* 3.5 7.3 - - - -
159N MET* 3.2 5.4 - - - +
160N TRP* 2.8 45.1 + - + -
162N SER 2.7 22.2 + - - -
163N VAL* 3.4 1.9 - - - -
164N LEU* 3.0 38.3 + - + -
169N ILE* 4.0 19.1 - - + -
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Residues in contact with LEU 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N PHE* 4.1 7.4 - - + -
34N THR* 1.3 75.4 - - - +
36N CYS* 1.3 62.5 + - - +
37N PHE* 3.7 22.5 - - + -
50N PHE* 3.5 53.8 - - + -
61N LEU* 5.6 2.9 - - + -
63N VAL* 4.0 13.5 - - + -
94N ILE 3.9 0.7 - - - +
95N CYS* 3.2 2.3 - - - -
96N VAL* 2.7 48.6 + - + +
157N LEU* 3.8 17.9 - - + -
158N TYR 3.4 14.6 - - - +
159N MET* 3.9 17.0 - - + -
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Residues in contact with CYS 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N THR* 4.1 7.9 - - - -
35N LEU* 1.3 75.5 - - - +
37N PHE* 1.3 66.7 + - - +
93N HIS* 4.2 8.1 - - + +
94N ILE 3.1 4.3 - - - -
95N CYS* 2.0 47.6 - - - -
156N ASP 3.2 2.8 - - - +
157N LEU* 3.3 1.4 - - - +
158N TYR* 2.7 39.3 + - + +
160N TRP* 3.6 28.9 - - + -
164N LEU* 4.8 0.9 - - - -
169N ILE* 4.6 2.5 - - - -
172N ALA* 4.5 7.6 - - + -
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Residues in contact with PHE 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N LEU* 3.7 27.4 - - + -
36N CYS* 1.3 80.0 - - - +
38N ARG* 1.3 73.3 + - - +
39N ALA* 4.3 4.0 + - + -
49N LEU* 3.6 39.9 - - + -
50N PHE* 4.6 5.4 - - + -
63N VAL* 4.2 7.0 - - + -
93N HIS* 3.6 6.5 + - - -
94N ILE* 2.8 73.7 + - + +
96N VAL* 5.6 0.4 - - + -
154N ILE* 4.6 8.1 - - + -
155N GLY 3.7 7.9 - - - +
156N ASP 3.3 10.3 - - - -
157N LEU* 3.6 28.5 - - + -
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Residues in contact with ARG 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N PHE* 1.3 73.4 - - - +
39N ALA* 1.3 62.0 + - - +
92N VAL 3.3 10.1 - - - +
93N HIS* 3.5 26.7 - - + +
154N ILE* 3.2 8.7 - - - +
155N GLY* 2.8 37.4 + - - +
156N ASP* 2.9 29.8 + - - +
172N ALA 3.2 18.4 + - - -
173N TYR* 2.8 34.8 + - - -
174N GLN 4.4 0.4 - - - -
175N GLY* 3.9 11.9 - - - +
201N LEU* 4.9 3.1 - - - -
203N TRP* 3.7 17.0 - - + -
204N VAL* 3.7 41.2 - - + +
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Residues in contact with ALA 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N PHE* 4.3 9.1 + - + -
38N ARG* 1.3 75.1 - - - +
40N TYR* 1.3 60.6 + - - +
41N SER 4.3 0.7 - - - +
47N TYR* 6.2 0.4 - - - +
49N LEU* 4.3 18.6 - - + -
90N ALA 4.2 0.7 - - - +
91N PRO* 3.5 2.4 - - - +
92N VAL* 2.9 48.4 + - + +
94N ILE* 4.7 0.9 - - + -
150N PHE* 4.4 4.9 - - + -
153N GLU 3.2 9.6 - - - +
154N ILE* 4.2 11.7 - - + -
203N TRP* 3.9 3.4 - - - -
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Residues in contact with TYR 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N ALA* 1.3 75.7 - - - +
41N SER* 1.3 63.1 + - - +
89N PRO* 4.7 7.7 + - + +
90N ALA* 3.7 13.2 - - - -
91N PRO* 3.5 34.4 - - + +
150N PHE* 4.5 0.2 - - - -
152N GLY* 3.4 3.6 - - - -
153N GLU* 2.8 38.9 + - + +
203N TRP* 3.6 52.9 - + + +
83O LYS 5.2 2.9 + - - -
112O THR* 5.2 3.6 - - - +
113O PRO 2.8 28.6 + - - -
114O LEU* 3.6 14.1 - - - +
115O VAL* 3.5 38.8 - - + +
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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