Contacts of the strand formed by residues 107 - 112 (chain A) in PDB entry 2WIN
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 TYR 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ARG* 5.2 0.9 + - - -
104A GLN* 5.4 2.7 - - - -
106A GLY* 1.3 79.3 - - - -
108A LEU* 1.3 64.8 + - - +
109A PHE* 4.0 22.2 - + + -
128A PHE 3.9 0.9 - - - +
130A VAL* 3.2 19.6 + - + +
131A ASN 3.4 13.7 - - - -
132A HIS* 3.7 45.6 + + - +
134A LEU* 4.2 12.6 - - + -
188A TYR* 3.0 19.6 + - - -
194A GLN* 4.8 5.6 - - - -
196A PHE* 3.5 13.2 - + + -
475A LYS 4.9 5.0 + - - -
597A VAL* 4.2 21.1 - - + -
598A VAL* 4.3 25.6 + - + +
601A ALA* 3.5 32.9 + - + +
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Residues in contact with LEU 108 (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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107A TYR* 1.3 75.8 - - - +
109A PHE* 1.3 68.8 + - - +
110A ILE* 4.2 2.3 + - + -
127A ILE* 4.1 9.9 - - + -
128A PHE 3.5 13.7 - - - +
129A THR* 3.6 15.5 - - + -
141A VAL* 4.3 5.8 - - + -
186A ALA* 3.9 10.1 - - + -
187A TYR* 3.6 38.1 - - - +
188A TYR* 3.4 44.0 - - + +
196A PHE* 3.4 46.3 - - + +
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Residues in contact with PHE 109 (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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107A TYR* 4.0 27.6 - + + -
108A LEU* 1.3 78.5 - - - +
110A ILE* 1.3 62.2 + - - +
126A ARG 3.5 0.9 - - - +
127A ILE* 3.6 1.0 - - - -
128A PHE* 2.9 57.5 + - + -
130A VAL* 4.0 19.5 - - + -
134A LEU* 4.5 7.9 - - + -
196A PHE* 6.4 0.4 - + - -
589A LEU* 4.6 17.9 - - + -
593A LYS 5.3 0.4 - - - -
594A ILE* 3.5 53.8 - - + -
597A VAL* 4.9 14.6 - - + -
598A VAL* 5.5 0.9 - - + -
793B ILE* 4.4 18.2 - - + -
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Residues in contact with ILE 110 (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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108A LEU* 4.2 4.2 + - + +
109A PHE* 1.3 76.2 - - - +
111A GLN* 1.3 64.1 + - - +
112A THR* 4.7 4.0 - - + -
125A TYR* 4.5 17.5 - - + -
126A ARG 3.5 7.4 - - - +
127A ILE* 4.3 13.7 - - + -
184A ILE* 3.2 50.3 - - + +
186A ALA* 4.1 15.3 - - + -
196A PHE* 4.1 15.7 - - + +
197A SER* 4.4 0.9 - - - -
198A THR* 3.3 41.0 + - - +
589A LEU* 4.6 11.6 - - - +
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Residues in contact with GLN 111 (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 ILE* 1.3 75.3 - - - +
112A THR* 1.3 73.4 + - - +
113A ASP 4.3 0.2 + - - -
124A LEU 3.7 1.0 - - - +
125A TYR* 3.0 5.4 - - - -
126A ARG* 2.9 59.3 + - - +
128A PHE* 3.3 30.1 - - + -
572A VAL* 4.4 1.4 + - - +
574A VAL* 3.6 28.5 - - - +
589A LEU* 3.8 28.0 - - + -
751B TRP* 4.3 4.0 - - - -
783B LEU* 3.8 20.6 + - + +
785B VAL* 4.5 6.4 - - - +
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Residues in contact with THR 112 (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 ILE* 4.3 7.1 + - + -
111A GLN* 1.3 83.3 + - - +
113A ASP* 1.3 66.7 + - - +
114A LYS 2.9 18.3 + - - +
115A THR* 4.9 1.0 - - - +
117A TYR* 3.4 15.7 - - - +
123A VAL* 4.4 5.6 - - + -
124A LEU 3.5 4.0 - - - -
125A TYR* 3.8 18.2 - - + -
184A ILE* 4.3 16.6 - - + -
198A THR* 5.0 13.7 - - + +
199A GLU 5.2 1.2 + - - -
200A PHE* 4.7 14.2 - - + +
587A ASN 5.1 4.5 + - - -
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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