Contacts of the strand formed by residues 104 - 109 (chain D) 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 ILE 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C VAL* 3.9 15.5 - - + -
12C PRO* 3.8 30.3 - - + -
195C TYR* 4.3 1.6 - - - +
197C ILE* 4.1 11.7 - - + -
199C LYS* 4.1 17.0 - - + -
97D SER* 3.9 0.9 + - - +
98D TRP* 3.3 4.3 - - - -
99D GLU* 3.2 26.6 + - + +
102D SER* 3.1 24.8 + - - +
103D GLY* 1.3 75.8 - - - +
105D ALA* 1.3 61.3 + - - +
106D GLU* 4.0 18.5 - - + +
116D LYS* 3.9 27.8 - - + -
117D LYS 3.3 11.2 - - - +
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Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D LEU* 3.7 29.6 - - + -
80D VAL* 4.0 19.5 - - + -
96D VAL* 5.2 1.8 - - + -
97D SER 3.2 5.2 - - - -
98D TRP* 4.1 1.8 - - + -
103D GLY 3.4 0.8 + - - -
104D ILE* 1.3 73.2 - - - +
106D GLU* 1.3 62.8 + - - +
107D PHE* 4.2 4.7 + - + -
115D VAL 4.7 1.0 - - - +
116D LYS* 3.7 5.2 - - - -
117D LYS* 2.7 33.5 + - - +
119D LEU* 4.0 8.1 - - + -
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Residues in contact with GLU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C LYS* 5.1 4.7 - - - +
202C VAL* 5.8 1.0 - - - +
95D CYS 3.7 0.5 - - - +
96D VAL* 3.2 6.7 - - - -
97D SER* 2.9 47.7 + - - +
104D ILE* 4.0 9.4 - - + +
105D ALA* 1.3 76.3 - - - +
107D PHE* 1.3 62.3 + - - +
108D TRP* 3.1 35.2 + - + +
114D LEU 5.6 1.3 - - - +
116D LYS* 3.3 46.0 + - + +
163D VAL* 4.7 9.9 - - - +
164D LEU 4.9 6.1 - - - +
166D PRO* 5.9 1.2 - - - +
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Residues in contact with PHE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D VAL* 4.1 17.5 - - + -
71D TYR* 3.6 40.4 - - + -
72D SER* 3.7 22.0 - - - -
73D LEU* 3.7 21.1 - - + -
80D VAL* 4.9 5.8 - - + -
82D SER* 4.4 11.7 - - - -
94D ILE* 4.2 14.4 - - + -
95D CYS 3.4 5.4 - - - -
96D VAL* 3.7 30.7 - - + -
105D ALA* 4.2 4.4 + - + -
106D GLU* 1.3 74.5 - - - +
108D TRP* 1.3 64.3 + - - +
109D ILE* 4.6 3.1 - - + -
113D PRO* 3.6 1.0 - - - +
114D LEU* 2.8 53.2 + - + +
115D VAL 5.4 2.0 + - - -
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Residues in contact with TRP 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C VAL* 4.0 17.5 - - + -
93D HIS* 3.4 2.6 + - - +
94D ILE* 3.4 5.2 - - - -
95D CYS* 2.7 43.3 + - + +
96D VAL* 5.4 0.2 - - - -
97D SER* 4.9 1.7 + - - -
106D GLU* 3.1 43.1 + - + +
107D PHE* 1.3 78.7 + - - +
109D ILE* 1.3 62.6 + - - +
111D GLY* 3.8 15.7 + - - +
112D THR 3.3 6.5 - - - +
113D PRO* 3.6 44.4 - - + -
116D LYS* 5.6 0.2 - - - -
164D LEU 5.5 0.4 + - - -
166D PRO* 3.7 40.8 - - + -
169D ILE* 3.6 45.6 - - + +
170D LEU* 4.6 8.1 - - + -
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Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D TYR* 3.8 23.1 - - + -
84D VAL* 4.2 21.2 - - + +
85D ILE 5.7 0.2 - - - +
86D GLU* 4.4 7.0 - - + +
92D VAL* 3.7 20.0 - - + -
93D HIS 3.4 0.9 - - - -
94D ILE* 3.8 32.1 - - + -
107D PHE* 4.6 6.1 - - + -
108D TRP* 1.3 78.9 - - - +
110D ASN* 1.3 78.3 + - - +
112D THR* 2.9 25.9 + - - -
114D LEU* 3.8 33.2 - - + -
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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