Contacts of the strand formed by residues 104 - 109 (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 ILE 104 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10M VAL* 4.0 16.2 - - + -
12M PRO* 3.9 29.2 - - + -
195M TYR* 4.5 1.3 - - - +
197M ILE* 4.1 18.8 - - + -
199M LYS* 4.2 11.2 - - + -
97N SER* 3.8 1.6 + - - +
98N TRP* 3.3 5.2 - - - -
99N GLU* 3.2 25.1 + - + +
102N SER* 3.2 26.4 + - - +
103N GLY* 1.3 76.2 - - - +
105N ALA* 1.3 65.3 + - - +
106N GLU* 4.2 6.6 + - + +
116N LYS* 3.8 33.7 - - + -
117N LYS 3.3 10.5 - - - +
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Residues in contact with ALA 105 (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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73N LEU* 3.8 28.3 - - + -
80N VAL* 3.9 21.1 - - + -
96N VAL* 5.3 1.1 - - + -
97N SER 3.3 5.2 - - - -
98N TRP* 4.5 1.3 - - + +
103N GLY 3.5 1.2 + - - -
104N ILE* 1.3 74.6 - - - +
106N GLU* 1.3 59.7 + - - +
107N PHE* 4.1 5.6 + - + -
115N VAL 4.7 0.9 - - - +
116N LYS* 3.7 6.6 - - - -
117N LYS* 2.6 34.3 + - + +
119N LEU* 4.1 8.1 - - + -
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Residues in contact with GLU 106 (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* 5.1 4.3 - - - +
202M VAL* 5.5 2.7 - - - +
95N CYS 3.6 0.5 - - - +
96N VAL* 3.2 6.8 - - - +
97N SER* 2.9 48.8 + - - +
104N ILE* 4.7 6.7 - - + +
105N ALA* 1.3 71.8 - - - +
107N PHE* 1.3 64.4 + - - +
108N TRP* 2.8 40.3 + - + +
113N PRO* 6.3 0.9 - - + -
114N LEU 5.6 2.7 - - - +
116N LYS* 3.3 46.6 + - + +
163N VAL* 5.1 7.1 - - - +
164N LEU 4.7 8.8 - - - +
166N PRO* 5.8 1.2 - - - +
169N ILE* 5.6 0.2 - - - +
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Residues in contact with PHE 107 (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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63N VAL* 4.3 10.1 - - + -
71N TYR* 3.6 40.8 - + + -
72N SER 3.6 22.2 - - - -
73N LEU* 3.8 21.3 - - + -
80N VAL* 4.9 6.3 - - + -
82N SER* 4.4 13.2 - - - +
94N ILE* 4.2 18.2 - - + -
95N CYS 3.4 10.5 - - - -
96N VAL* 3.7 25.1 - - + -
105N ALA* 4.1 4.8 - - + -
106N GLU* 1.3 75.8 - - - +
108N TRP* 1.3 58.9 + - - +
109N ILE* 4.7 2.2 - - + -
113N PRO* 3.6 3.5 - - - +
114N LEU* 2.8 56.6 + - + +
115N VAL 5.4 2.2 + - - -
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Residues in contact with TRP 108 (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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202M VAL* 4.1 19.7 - - + -
93N HIS* 3.4 5.9 + - - +
94N ILE* 3.5 1.9 - - - -
95N CYS* 2.7 42.7 + - + +
97N SER* 5.5 1.1 - - - -
106N GLU* 2.8 44.8 + - + +
107N PHE* 1.3 76.7 + - - +
109N ILE* 1.3 64.1 + - - +
110N ASN 4.0 0.2 - - - -
111N GLY* 3.7 21.5 + - - +
112N THR 3.3 5.8 - - - +
113N PRO* 3.6 45.3 - - + -
166N PRO* 3.7 42.2 - - + -
169N ILE* 3.6 45.0 - - + +
170N LEU* 5.5 4.9 - - + -
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Residues in contact with ILE 109 (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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71N TYR* 3.5 35.0 - - + -
84N VAL* 4.2 25.1 - - + -
85N ILE 5.7 0.7 - - - +
86N GLU* 4.4 6.7 - - + +
92N VAL* 3.7 18.4 - - + -
93N HIS 3.4 1.3 - - - -
94N ILE* 3.9 20.2 - - + -
107N PHE* 4.7 4.0 - - + -
108N TRP* 1.3 77.8 - - - +
110N ASN* 1.3 74.5 - - - +
112N THR* 2.8 37.7 + - - +
114N LEU* 3.8 28.0 - - + -
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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