Contacts of the strand formed by residues 92 - 99 (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 VAL 92 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N PHE 4.1 0.2 - - - +
38N ARG* 3.3 7.9 - - - +
39N ALA* 2.9 47.7 + - + +
71N TYR* 3.6 22.7 - - + +
86N GLU* 4.5 4.5 - - + +
90N ALA 4.3 5.4 - - - +
91N PRO* 1.3 75.0 - - - +
93N HIS* 1.3 66.5 + - - +
94N ILE* 3.6 25.8 - - + -
109N ILE* 3.7 25.4 - - + -
110N ASN* 3.5 9.2 - - - +
203N TRP* 4.9 0.6 - - - -
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Residues in contact with HIS 93 (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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36N CYS* 4.2 7.4 - - + +
37N PHE* 3.6 10.5 + - - -
38N ARG* 3.5 40.6 - - + +
92N VAL* 1.3 76.0 - - - +
94N ILE* 1.3 65.6 + - - +
95N CYS* 3.5 31.5 - - - -
108N TRP 3.4 5.1 + - - +
109N ILE* 3.4 3.1 - - - -
110N ASN* 2.8 40.1 + - - +
111N GLY 5.1 1.8 + - - -
156N ASP* 5.2 4.0 + - + +
169N ILE* 6.0 0.4 - - - +
172N ALA* 3.5 16.3 + - - +
173N TYR* 3.5 48.0 - + + +
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Residues in contact with ILE 94 (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 3.9 0.7 - - - +
36N CYS* 3.1 3.8 - - - +
37N PHE* 2.8 80.9 + - + +
39N ALA* 4.7 2.2 - - + -
49N LEU* 4.3 9.4 - - + -
63N VAL* 5.0 2.2 - - + -
71N TYR* 3.6 19.1 - - + -
92N VAL* 3.6 27.8 - - + -
93N HIS* 1.3 76.9 - - - +
95N CYS* 1.3 75.1 + - - +
96N VAL* 4.8 1.8 - - + +
107N PHE* 4.2 20.2 - - + -
108N TRP 3.5 2.7 - - - -
109N ILE* 3.9 18.6 - - + -
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Residues in contact with CYS 95 (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 3.2 3.6 - - - -
36N CYS* 2.0 45.3 - - - -
93N HIS* 3.5 19.5 - - - -
94N ILE* 1.3 73.5 - - - +
96N VAL* 1.3 60.8 + - - +
106N GLU 4.2 0.9 - - - -
107N PHE* 3.4 6.1 - - - -
108N TRP* 2.7 53.2 + - + +
169N ILE* 3.8 30.7 - - + -
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Residues in contact with VAL 96 (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* 3.8 10.5 - - + -
34N THR* 3.5 2.6 - - - -
35N LEU* 2.7 53.7 + - + +
36N CYS* 4.9 0.2 - - - -
37N PHE* 5.6 0.7 - - + -
63N VAL* 3.8 27.4 - - + -
73N LEU* 3.8 25.1 - - + -
94N ILE* 5.3 2.9 - - + -
95N CYS* 1.3 76.2 - - - +
97N SER* 1.3 65.2 + - - +
106N GLU 3.2 10.8 - - - +
107N PHE* 3.7 35.9 - - + -
169N ILE* 6.3 0.2 - - - -
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Residues in contact with SER 97 (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* 3.2 15.0 - - - -
34N THR* 3.5 18.2 - - - -
96N VAL* 1.3 78.2 - - - +
98N TRP* 1.3 61.6 + - - +
104N ILE 4.3 0.7 + - - -
105N ALA* 3.3 5.7 - - - +
106N GLU* 2.9 52.0 + - - +
108N TRP* 5.2 1.0 + - - -
163N VAL* 3.5 22.3 - - - +
164N LEU 4.9 2.0 + - - -
169N ILE* 5.6 4.0 - - - -
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Residues in contact with TRP 98 (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 3.8 4.0 - - - -
31N GLN 3.5 22.9 - - - -
32N ASN* 3.5 5.7 - - - -
33N PHE* 3.1 63.2 + + + +
73N LEU* 4.3 5.2 - - + -
75N ILE* 3.8 29.1 - - + +
97N SER* 1.3 76.2 - - - +
99N GLU* 1.3 65.2 + - - +
100N SER* 3.6 9.9 - - - -
103N GLY 3.5 18.7 + - - -
104N ILE 3.3 7.9 - - - -
105N ALA* 4.4 1.6 - - + -
119N LEU* 3.1 35.8 + - + +
120N ARG 3.2 22.4 - - - -
123N TYR* 3.2 28.9 - + - -
125N VAL* 3.5 20.9 - - + -
163N VAL* 3.8 4.5 - - - +
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Residues in contact with GLU 99 (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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199M LYS* 2.7 32.3 + - - -
32N ASN* 3.7 17.2 - - - +
98N TRP* 1.3 77.7 - - - +
100N SER* 1.3 54.2 + - - +
101N SER* 3.5 20.9 + - - +
102N SER* 2.8 19.7 + - - +
103N GLY* 2.6 36.9 + - - -
104N ILE* 3.2 10.5 + - + +
163N VAL* 3.8 20.3 - - + +
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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