Contacts of the strand formed by residues 122 - 130 (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 THR 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ASP* 4.6 2.4 - - - +
114A LYS* 5.4 1.2 - - - -
117A TYR* 3.9 11.2 - - - -
120A GLY 5.1 0.7 + - - -
121A SER* 1.3 78.0 + - - +
123A VAL* 1.3 67.8 + - - +
124A LEU* 3.9 26.9 + - + +
170A SER* 4.2 4.7 - - - -
171A TRP 3.7 11.0 - - - +
172A ASP* 3.2 35.9 + - - +
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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
----------------------------------------------------------
112A THR* 4.4 9.6 - - + -
117A TYR* 3.5 44.4 - - + +
122A THR* 1.3 71.6 - - - +
124A LEU* 1.3 66.7 + - - +
125A TYR* 3.7 17.2 - - + -
170A SER* 3.1 6.4 - - - -
171A TRP* 2.9 40.0 + - + +
173A ILE* 3.6 30.1 - - + -
184A ILE* 4.8 5.6 - - + -
200A PHE* 4.0 14.6 - - + -
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR* 3.5 1.7 - - - -
113A ASP* 2.8 51.8 + - + +
122A THR* 4.1 15.5 - - + +
123A VAL* 1.3 74.5 - - - +
125A TYR* 1.3 59.8 + - - +
169A LEU 3.7 3.4 - - - +
170A SER* 3.6 25.1 - - - -
748B SER* 5.5 6.5 - - - +
751B TRP* 3.5 53.9 - - + +
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Residues in contact with TYR 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 ILE* 4.5 4.5 - - + -
111A GLN 3.0 10.8 - - - +
112A THR* 3.8 18.2 - - + -
123A VAL* 3.7 14.6 - - + -
124A LEU* 1.3 74.4 - - - +
126A ARG* 1.3 61.5 + - - +
127A ILE* 3.4 17.7 - - + -
143A VAL* 4.0 16.2 - - + +
145A ILE* 3.9 26.8 - - + +
154A LYS* 4.0 13.5 + - - -
156A ASP* 4.1 4.7 + - - -
167A LEU 3.8 0.2 - - - +
169A LEU* 2.9 63.1 + - + +
170A SER* 3.7 22.0 - - - -
171A TRP* 4.1 2.5 - - + -
184A ILE* 4.0 22.0 - - + -
751B TRP* 4.4 0.2 - - - -
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Residues in contact with ARG 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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109A PHE 3.5 4.3 - - - +
110A ILE* 3.5 2.4 - - - +
111A GLN* 2.9 64.8 + - - +
125A TYR* 1.3 72.5 - - - +
127A ILE* 1.3 61.9 + - - +
128A PHE* 4.1 7.5 - - + -
166A VAL* 3.9 23.3 - - + -
167A LEU 3.4 5.4 - - - +
168A PRO* 3.7 22.7 - - + -
572A VAL* 3.4 34.9 - - - +
573A LEU 3.4 22.0 + - - -
751B TRP* 3.0 60.0 - - + +
752B ASN 4.4 4.4 + - - -
753B VAL* 4.8 4.5 - - - +
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Residues in contact with ILE 127 (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* 4.1 27.6 - - + -
109A PHE 3.6 4.7 - - - +
110A ILE* 4.3 18.6 - - + -
125A TYR* 3.4 39.5 - - + -
126A ARG* 1.3 74.2 - - - +
128A PHE* 1.3 63.0 + - - +
129A THR* 3.7 9.2 + - + -
141A VAL* 4.4 12.8 - - + -
143A VAL* 4.2 14.6 - - + -
166A VAL* 3.8 0.9 - - - -
167A LEU* 3.0 46.1 + - + +
169A LEU* 3.7 16.6 - - + -
186A ALA* 4.6 6.7 - - + -
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Residues in contact with PHE 128 (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 3.9 0.7 - - - +
108A LEU* 3.5 11.4 - - - +
109A PHE* 2.9 62.4 + - + +
111A GLN* 3.3 41.1 - - + -
126A ARG* 4.3 9.2 - - + -
127A ILE* 1.3 73.6 - - - +
129A THR* 1.3 60.8 + - - +
130A VAL* 4.0 1.7 + - + -
165A GLY 3.4 2.0 - - - -
166A VAL* 3.9 26.2 - - + -
572A VAL* 4.1 12.3 - - + -
589A LEU* 4.0 10.3 - - + -
785B VAL* 3.7 26.0 - - + -
787B MET* 3.6 28.5 - - + -
793B ILE* 4.1 11.2 - - + -
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Residues in contact with THR 129 (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* 3.6 18.6 - - + -
127A ILE* 4.2 11.9 - - + +
128A PHE* 1.3 72.7 - - - +
130A VAL* 1.3 65.4 + - - +
136A PRO* 3.5 2.8 - - - +
137A VAL* 3.0 33.6 + - - -
141A VAL* 3.6 23.3 - - + -
160A SER* 3.0 19.7 + - - +
165A GLY* 3.2 20.5 + - - -
167A LEU* 4.3 2.0 - - + -
188A TYR* 3.5 15.7 - - + -
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Residues in contact with VAL 130 (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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106A GLY* 3.6 1.9 - - - -
107A TYR* 3.2 27.6 + - + +
109A PHE* 4.0 25.4 - - + -
128A PHE* 5.0 1.8 - - + +
129A THR* 1.3 81.7 - - - +
131A ASN* 1.3 66.7 + - - +
134A LEU* 3.4 31.2 - - + +
135A LEU 3.4 9.0 - - - +
136A PRO 3.8 9.6 - - - -
137A VAL* 3.9 6.9 - - - +
188A TYR* 3.0 15.5 + - - -
787B MET* 3.8 23.8 - - + -
793B ILE* 4.7 4.0 - - + -
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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