Contacts of the strand formed by residues 138 - 143 (chain A) in PDB entry 1YCH
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 SER 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A SER* 5.4 6.7 + - - -
132A VAL 3.2 16.8 - - - -
133A SER* 3.8 13.5 - - - +
134A LEU* 4.2 4.4 - - - +
137A ARG* 1.3 76.0 - - - +
139A LEU* 1.3 66.9 + - - +
140A THR* 4.2 0.6 - - - +
157A VAL* 3.5 19.9 - - - +
158A PRO* 3.7 8.4 - - - +
159A GLU* 2.5 32.4 + - - +
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Residues in contact with LEU 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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42A ILE* 4.0 14.4 - - + -
48A ALA* 4.0 19.1 - - + -
78A VAL* 4.6 7.9 - - + -
103A LEU* 4.0 8.7 - - + -
131A SER* 4.4 1.6 - - - -
132A VAL* 2.9 46.6 + - + +
134A LEU* 3.5 31.2 - - + -
138A SER* 1.3 74.9 - - - +
140A THR* 1.3 61.1 + - - +
141A PHE* 3.0 36.4 - - + -
155A THR* 4.1 14.1 - - + -
156A TYR 3.4 7.4 - - - +
157A VAL* 4.5 4.3 - - + -
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Residues in contact with THR 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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129A GLY* 4.6 6.2 + - - -
130A THR 3.5 11.5 + - - -
131A SER* 3.9 11.7 - - - -
138A SER* 5.5 0.9 - - - +
139A LEU* 1.3 74.5 - - - +
141A PHE* 1.3 75.8 + - - +
142A ILE* 5.1 2.9 - - - +
155A THR* 3.6 1.2 - - - +
156A TYR* 2.8 48.1 + - + +
158A PRO* 3.2 35.7 - - + -
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Residues in contact with PHE 141 (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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78A VAL* 3.8 16.8 - - + -
103A LEU* 4.0 14.6 - - + -
126A VAL* 3.4 42.2 - - + -
127A LYS 4.3 1.6 - - - +
128A THR* 4.2 1.6 - - - -
129A GLY 2.9 25.9 + - - -
130A THR* 3.2 12.0 + - - -
132A VAL* 4.4 11.7 - - + -
139A LEU* 3.0 43.3 - - + -
140A THR* 1.3 79.5 + - - +
142A ILE* 1.3 69.5 + - - +
143A GLU* 4.2 0.9 - - + -
153A MET* 3.8 21.1 - - + -
154A PHE 3.6 4.0 - - - +
155A THR* 3.4 33.2 - - + -
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Residues in contact with ILE 142 (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 THR* 3.9 8.3 - - + -
140A THR* 5.1 4.3 - - - +
141A PHE* 1.3 80.5 - - - +
143A GLU* 1.3 75.3 + - - +
144A ALA* 4.3 0.3 - - - +
153A MET* 3.3 3.4 - - - +
154A PHE* 2.7 56.3 + - + +
156A TYR* 5.0 11.4 - - + -
163A LEU* 5.2 2.9 - - + -
210A LYS* 4.4 11.2 - - + -
213A GLU* 3.7 22.2 - - - +
214A ILE* 4.6 15.7 - - + -
217A ILE* 5.3 6.5 - - + -
219A LEU* 3.5 32.3 - - + -
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Residues in contact with GLU 143 (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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105A THR* 5.0 13.0 - - + +
126A VAL* 4.2 6.3 - - + +
127A LYS* 3.1 33.9 - - - +
128A THR* 2.6 44.6 + - - +
141A PHE* 6.2 0.4 - - + -
142A ILE* 1.3 79.1 - - - +
144A ALA* 1.3 59.0 + - - +
145A PRO* 3.4 14.0 - - + +
152A SER 4.3 1.1 - - - +
153A MET* 3.9 9.2 - - + -
210A LYS* 2.8 22.0 + - - -
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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