Contacts of the strand formed by residues 122 - 132 (chain A) in PDB entry 1BY7
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 LEU 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LEU* 1.3 60.4 + - - +
124A GLU* 4.0 20.6 - - - +
203A TYR* 4.2 22.2 - - + +
204A PHE* 3.1 14.5 - - - -
205A LYS* 2.8 63.9 + - + +
206A GLY* 4.6 3.4 - - - -
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Residues in contact with LEU 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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33A TRP* 4.2 31.6 - - + -
114A ILE* 4.2 22.0 - - + +
115A ASN* 4.2 14.8 - - - +
122A LEU* 1.3 73.3 - - - +
124A GLU* 1.3 65.1 + - - +
125A SER* 4.2 0.7 + - - -
202A VAL* 4.6 2.0 - - + -
203A TYR 3.5 1.8 - - - +
204A PHE* 3.9 12.3 - - + -
407A LEU* 4.3 14.1 - - + -
408A PHE* 3.6 37.9 - - + -
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Residues in contact with GLU 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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122A LEU* 4.0 26.9 - - - +
123A LEU* 1.3 78.6 - - - +
125A SER* 1.3 60.3 + - - +
126A VAL* 5.5 5.4 - - + -
178A LYS* 4.7 19.1 + - - +
180A LYS* 4.1 17.8 + - - -
201A ALA 4.6 0.4 - - - -
202A VAL* 3.1 7.6 - - - +
203A TYR* 2.6 56.2 + - + +
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 4.4 18.6 - - - -
34A SER* 3.9 8.0 - - - -
123A LEU 4.2 1.0 + - - -
124A GLU* 1.3 75.7 - - - +
126A VAL* 1.3 67.7 + - - +
127A ASN* 5.2 6.7 + - - -
200A ASN* 3.6 8.1 + - - -
201A ALA 3.6 4.0 - - - -
202A VAL* 3.3 24.0 - - - +
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Residues in contact with VAL 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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124A GLU* 5.5 4.0 - - + -
125A SER* 1.3 80.9 + - - +
127A ASN* 1.3 62.3 + - - +
172A TRP* 4.2 17.9 - - + -
173A VAL* 5.6 2.5 - - + +
176A GLN* 3.6 38.6 - - + +
177A THR* 4.1 14.4 - - + -
199A VAL* 4.6 0.3 - - - +
200A ASN* 3.3 5.2 - - - +
201A ALA* 3.0 54.1 + - + +
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Residues in contact with ASN 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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38A THR* 3.5 34.6 - - + +
41A MET* 4.7 6.9 - - - +
125A SER* 5.2 6.7 + - - -
126A VAL* 1.3 79.4 - - - +
128A LYS* 1.3 68.2 + - - +
149A TYR* 5.0 5.7 + - - +
151A SER* 2.7 38.3 + - - -
172A TRP* 3.4 13.2 - - - -
198A LEU* 5.0 1.2 - - + +
199A VAL 3.3 10.8 - - - +
200A ASN* 4.1 3.1 - - - +
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Residues in contact with LYS 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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127A ASN* 1.3 81.4 + - - +
129A LEU* 1.3 65.9 + - - +
130A PHE* 3.5 37.6 - - + -
151A SER* 4.7 2.7 - - - -
152A GLU* 2.6 46.1 + - - +
154A GLN* 4.0 18.6 + - + +
172A TRP* 3.5 46.2 - - + +
198A LEU* 3.6 5.7 - - - +
199A VAL* 2.9 37.5 + - - +
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Residues in contact with LEU 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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41A MET* 4.0 21.4 - - + +
42A VAL* 4.2 18.8 - - + -
128A LYS* 1.3 74.3 - - - +
130A PHE* 1.3 60.5 + - - +
131A GLY 4.1 0.2 + - - -
137A PHE* 3.9 23.1 - - + -
141A TYR* 3.7 27.1 - - + +
151A SER* 5.1 1.2 + - - -
152A GLU 5.1 0.2 + - - -
153A PRO* 3.2 12.9 - - + +
154A GLN 2.9 25.8 + - - -
196A MET* 3.7 28.7 - - + -
197A VAL 3.7 13.2 - - - +
198A LEU* 4.2 7.9 - - + +
343A MET* 3.9 13.7 - - + -
351A LEU* 4.8 1.8 - - + -
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Residues in contact with PHE 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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128A LYS* 3.5 39.7 - - + -
129A LEU* 1.3 74.1 - - - +
131A GLY* 1.3 58.5 + - - +
137A PHE* 4.4 2.5 - - - -
154A GLN* 3.2 44.9 - - + +
156A VAL* 4.0 10.3 - - + -
158A PHE* 3.9 7.8 - - + -
168A LYS 5.1 0.7 - - - -
169A ILE* 3.6 58.1 - - + -
172A TRP* 4.3 13.9 - + + -
196A MET* 3.3 4.8 - - - +
197A VAL* 3.0 46.6 + - + +
199A VAL* 3.9 10.5 - - + -
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Residues in contact with GLY 131 (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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130A PHE* 1.3 75.9 - - - +
132A GLU* 1.3 63.7 + - - -
133A LYS 3.2 0.2 + - - -
135A ALA 5.8 0.7 - - - -
137A PHE* 3.7 22.0 - - - -
154A GLN 3.0 9.1 + - - -
155A ALA* 3.3 6.2 - - - -
156A VAL* 2.8 27.9 + - - +
158A PHE* 4.1 3.1 - - - -
195A ARG 3.5 7.6 - - - -
196A MET* 4.3 2.9 - - - -
349A LEU* 5.3 2.0 - - - -
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Residues in contact with GLU 132 (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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131A GLY* 1.3 73.3 - - - -
133A LYS* 1.3 62.6 + - - +
134A SER* 2.4 40.3 + - - +
135A ALA* 3.0 32.9 + - + +
136A SER* 5.0 0.2 - - - -
156A VAL 3.4 3.9 - - - +
157A ASP* 3.8 2.6 - - - +
158A PHE* 2.8 44.2 + - + -
159A LEU* 3.0 25.8 + - - +
195A ARG* 2.9 45.2 + - - +
346A ARG* 4.1 2.5 - - - +
349A LEU* 5.3 0.6 - - - +
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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