Contacts of the strand formed by residues 121 - 126 (chain A) in PDB entry 3S8W
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ILE* 3.9 18.8 - - + -
115A VAL 3.6 10.8 - - - +
116A GLY* 4.3 3.6 - - - -
120A HIS* 1.3 77.8 - - - +
122A ASN* 1.3 65.8 + - - +
123A VAL* 3.5 21.1 + - + +
145A GLU* 6.3 0.9 - - + -
168A TYR 3.8 0.3 - - - +
169A ILE* 3.5 2.9 - - - -
170A ILE* 2.7 42.4 + - + +
173A LEU* 3.7 16.2 - - + -
179A TYR* 3.8 29.6 - - + +
181A VAL* 4.5 14.4 - - + -
201A THR* 4.0 16.2 - - + -
203A LEU* 3.9 12.8 - - + -
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Residues in contact with ASN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ILE* 3.4 1.2 - - - -
115A VAL* 2.8 42.5 + - + +
117A PHE* 3.5 14.6 - - - -
120A HIS* 2.8 24.6 + - - -
121A ILE* 1.3 71.8 - - - +
123A VAL* 1.3 61.1 + - - +
124A MSE 3.3 22.8 - - - +
167A THR* 4.5 4.0 - - + +
168A TYR 4.1 2.2 - - - -
169A ILE* 3.8 21.5 - - - +
167C THR 2.9 26.1 + - - -
168C TYR* 4.0 12.5 - - - +
169C ILE* 4.7 2.8 - - - +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 4.3 17.9 - - + -
113A GLU 3.6 7.6 - - - +
114A ILE* 4.0 7.4 - - + -
121A ILE* 3.8 19.7 - - + +
122A ASN* 1.3 74.8 - - - +
124A MSE 1.3 63.8 + - - +
125A VAL* 4.0 10.5 + - + +
143A ILE* 4.2 26.2 - - + -
166A PHE 3.9 0.5 - - - +
167A THR* 3.3 4.9 - - - +
168A TYR* 2.7 49.6 + - - +
170A ILE* 3.9 21.1 - - + -
181A VAL* 4.4 5.8 - - + -
183A VAL* 4.6 2.7 - - + -
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Residues in contact with MSE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.1 6.4 - - - +
113A GLU* 2.8 60.3 + - + +
114A ILE 4.1 1.1 - - - -
115A VAL* 3.5 24.0 - - + +
122A ASN* 3.3 43.1 - - - +
123A VAL* 1.3 71.6 - - - +
125A VAL* 1.3 61.2 + - - +
126A LYS 4.3 0.2 + - - -
166A PHE 3.8 3.8 - - - +
167A THR* 3.4 23.3 - - - +
178B ASN* 4.9 3.4 - - - +
168C TYR* 6.3 0.4 - - - -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PRO* 4.1 16.6 - - + -
111A GLU 3.5 9.9 - - - +
112A PHE* 4.3 1.8 - - + -
123A VAL* 4.3 10.1 - - + +
124A MSE 1.3 76.3 - - - +
126A LYS* 1.3 71.8 + - - +
127A PHE* 4.0 2.7 - - - +
141A LEU* 4.2 9.9 - - + -
143A ILE* 4.2 16.6 - - + -
165A ASN* 3.3 25.7 + - - +
166A PHE* 3.2 54.8 + - + +
183A VAL* 4.6 10.8 - - + -
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PRO* 3.8 3.6 - - - +
111A GLU* 2.8 45.1 + - + +
124A MSE 4.3 0.2 + - - -
125A VAL* 1.3 74.4 - - - +
127A PHE* 1.3 61.1 + - - +
165A ASN* 4.0 21.8 - - - +
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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