Contacts of the strand formed by residues 104 - 109 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97F SER* 4.0 0.9 + - - +
98F TRP* 3.3 4.4 - - - -
99F GLU* 3.1 26.3 + - + +
102F SER* 3.1 26.9 + - - +
103F GLY* 1.3 76.2 - - - +
105F ALA* 1.3 60.2 + - - +
106F GLU* 4.1 16.0 + - + +
116F LYS* 4.0 30.1 - - + -
117F LYS 3.3 10.3 - - - +
10J VAL* 3.8 15.7 - - + -
12J PRO* 3.8 31.0 - - + -
195J TYR* 4.4 1.3 - - - +
197J ILE* 4.0 16.8 - - + -
199J LYS* 4.0 11.2 - - + -
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Residues in contact with ALA 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F LEU* 3.8 25.1 - - + -
80F VAL* 4.0 19.3 - - + -
96F VAL* 5.2 1.6 - - + -
97F SER 3.2 10.3 - - - +
98F TRP* 4.2 1.1 - - + -
103F GLY 3.5 0.8 + - - -
104F ILE* 1.3 72.8 - - - +
106F GLU* 1.3 63.5 + - - +
107F PHE* 4.2 3.9 + - + -
115F VAL 4.6 0.7 - - - +
116F LYS* 3.6 6.1 - - - -
117F LYS* 2.6 35.0 + - - +
119F LEU* 4.1 7.6 - - + -
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Residues in contact with GLU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F CYS 3.7 0.5 - - - +
96F VAL* 3.2 8.3 - - - -
97F SER* 3.0 45.6 + - - +
104F ILE* 4.1 9.8 - - + +
105F ALA* 1.3 73.0 - - - +
107F PHE* 1.3 60.4 + - - +
108F TRP* 3.1 34.9 + - - +
113F PRO* 6.5 0.2 - - + -
114F LEU 5.7 2.2 - - - +
116F LYS* 3.3 47.9 - - + +
163F VAL* 4.8 9.1 - - - +
164F LEU 5.0 6.6 - - - +
166F PRO* 6.1 0.5 - - - +
199J LYS* 5.0 6.2 - - - +
202J VAL* 5.9 0.6 - - - +
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Residues in contact with PHE 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F VAL* 4.1 16.8 - - + -
71F TYR* 3.5 40.6 - - + -
72F SER 3.6 23.1 - - - -
73F LEU* 3.7 20.2 - - + -
80F VAL* 4.8 7.4 - - + -
82F SER* 4.5 11.9 - - - -
94F ILE* 4.3 12.8 - - + -
95F CYS 3.4 4.5 - - - -
96F VAL* 3.6 31.2 - - + -
105F ALA* 4.2 3.5 + - + -
106F GLU* 1.3 74.8 - - - +
108F TRP* 1.3 63.0 + - - +
109F ILE* 4.2 3.8 - - + -
113F PRO* 3.6 3.1 - - - +
114F LEU* 2.8 52.4 + - + +
115F VAL 5.4 1.8 + - - -
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Residues in contact with TRP 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F HIS* 3.5 2.1 + - - +
94F ILE* 3.4 5.9 - - - -
95F CYS* 2.7 44.0 + - + +
97F SER* 5.2 2.2 + - - -
106F GLU* 3.1 41.2 + - + +
107F PHE* 1.3 79.2 + - - +
109F ILE* 1.3 62.8 + - - +
110F ASN 4.0 0.4 + - - -
111F GLY* 3.6 20.1 + - - +
112F THR 3.3 5.2 - - - +
113F PRO* 3.6 45.1 - - + -
164F LEU 6.0 0.2 - - - -
166F PRO* 3.9 39.5 - - + -
169F ILE* 3.6 45.0 - - + +
170F LEU* 5.5 3.4 - - + -
202J VAL* 4.1 20.6 - - + -
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Residues in contact with ILE 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F TYR* 3.8 33.4 - - + -
84F VAL* 4.3 19.2 - - + +
85F ILE 5.7 0.4 - - - +
86F GLU* 4.3 14.1 - - + +
92F VAL* 3.6 20.2 - - + -
93F HIS 3.4 1.1 - - - -
94F ILE* 4.0 19.7 - - + -
107F PHE* 4.6 7.6 - - + -
108F TRP* 1.3 79.3 - - - +
110F ASN* 1.3 79.7 + - - +
112F THR* 2.8 31.4 + - - +
114F LEU* 3.8 25.6 - - + -
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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