Contacts of the strand formed by residues 133 - 140 (chain A) in PDB entry 1Y67
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 GLY 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ARG* 4.0 2.7 - - - -
131A GLY 4.0 1.2 + - - -
132A SER* 1.3 77.2 - - - +
134A TRP* 1.3 69.7 + - - -
149A THR 3.1 11.9 - - - -
151A ASN 3.5 15.5 - - - -
174A VAL* 2.9 34.2 + - - +
175A TRP* 3.4 9.0 - - - +
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Residues in contact with TRP 134 (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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80A ASN* 3.5 42.8 - - + +
81A HIS* 3.8 15.0 - + - -
84A PHE* 3.8 28.0 - + + -
129A ARG* 4.3 1.4 - - - +
133A GLY* 1.3 81.5 - - - -
135A ALA* 1.3 59.3 + - - +
136A TRP* 3.5 39.2 + + + +
148A SER* 3.2 7.0 - - - -
149A THR* 2.9 34.3 + - - +
151A ASN 3.2 22.9 + - - -
152A GLN* 2.9 19.8 + - - -
153A ASP 4.6 0.2 - - - -
171A GLY* 4.2 3.1 - - - -
172A VAL 3.3 25.8 - - - -
173A ASP* 3.5 41.3 + - + -
174A VAL* 4.0 4.7 - - - +
175A TRP* 3.9 4.4 - - - +
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Residues in contact with ALA 135 (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 PHE* 3.7 14.6 - - + +
125A ALA* 4.3 5.2 - - + -
126A ALA* 3.7 39.5 - - + +
134A TRP* 1.3 73.9 - - - +
136A TRP* 1.3 62.0 + - - +
147A VAL 3.5 9.0 - - - +
148A SER* 4.2 1.1 - - - -
171A GLY* 3.1 4.7 - - - -
172A VAL* 3.0 39.2 + - + +
174A VAL* 4.9 1.4 - - - +
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Residues in contact with TRP 136 (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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80A ASN* 3.4 35.0 - - + -
83A MET* 3.9 22.7 - - - -
122A PHE* 3.7 6.0 - - - -
134A TRP* 3.5 38.9 - + + +
135A ALA* 1.3 79.3 - - - +
137A LEU* 1.3 59.9 + - - +
138A VAL* 3.9 17.7 + - + -
145A ASP 3.8 0.2 - - - +
146A VAL* 3.3 9.5 - - - +
147A VAL* 2.8 39.1 + - + +
149A THR* 2.8 28.3 + - + -
153A ASP 3.8 8.7 - - - -
154A ASN* 3.5 10.1 - - - -
155A PRO* 3.5 24.4 - - + +
168A PRO* 3.5 19.1 - - + -
170A LEU 3.3 5.4 - - - +
171A GLY* 3.7 21.5 - - - -
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Residues in contact with LEU 137 (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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104A LEU* 5.0 1.3 - - + -
108A ILE* 4.8 10.5 - - + -
112A PHE* 3.8 27.1 - - + -
118A PHE* 3.8 34.1 - - + -
122A PHE* 3.8 3.2 - - + -
136A TRP* 1.3 70.6 - - - +
138A VAL* 1.3 60.0 + - - +
144A LEU* 3.9 15.5 - - + -
145A ASP 3.5 14.8 - - - +
146A VAL* 4.2 1.3 - - + -
168A PRO* 3.5 2.6 - - - +
169A ILE* 2.9 53.1 + - + +
170A LEU* 2.8 28.4 + - + -
200A TRP* 4.7 10.1 - - + -
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Residues in contact with VAL 138 (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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136A TRP* 3.9 9.0 - - + -
137A LEU* 1.3 76.9 - - - +
139A VAL* 1.3 62.3 + - - +
140A LYS* 4.5 5.4 - - + -
143A LYS 3.6 0.5 - - - +
144A LEU* 3.3 8.3 - - - +
145A ASP* 3.0 54.6 + - + +
147A VAL* 3.9 12.6 - - + -
155A PRO* 3.8 30.3 - - + -
165A SER 3.7 16.2 - - - +
166A GLY* 4.0 7.0 - - - -
167A THR 3.2 9.0 - - - +
168A PRO* 3.8 17.5 - - + -
169A ILE* 5.1 0.7 - - - -
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Residues in contact with VAL 139 (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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138A VAL* 1.3 70.4 - - - +
140A LYS* 1.3 60.6 + - - +
141A ASP 4.2 0.4 + - - -
142A GLY* 3.8 32.3 - - - +
143A LYS 3.4 4.5 - - - +
144A LEU* 3.8 11.9 - - + -
166A GLY* 3.5 0.9 - - - -
167A THR* 2.9 34.9 + - - +
169A ILE* 4.1 10.8 - - + -
207A TYR* 3.8 28.3 - - + -
210A ALA* 3.9 37.7 - - + +
211A LYS* 4.7 5.4 - - + -
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Residues in contact with LYS 140 (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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138A VAL* 3.9 7.4 - - + -
139A VAL* 1.3 74.2 - - - +
141A ASP* 1.3 93.9 + - - +
143A LYS* 2.8 27.2 + - - +
145A ASP* 5.2 8.1 - - + +
165A SER* 2.9 36.4 + - - +
166A GLY* 4.0 15.7 - - - +
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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