Contacts of the strand formed by residues 115 - 126 (chain A) in PDB entry 1YC9
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 ASP 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ALA* 4.6 5.9 - - - +
113A SER* 4.1 9.9 + - - +
114A PHE* 1.3 79.2 - - - +
116A LEU* 1.3 63.6 + - - +
149A ASN 4.4 0.2 - - - -
150A PHE* 3.2 7.1 - - - -
151A GLN* 2.9 42.9 + - + +
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Residues in contact with LEU 116 (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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114A PHE* 3.9 24.0 - - + -
115A ASP* 1.3 76.2 - - - +
117A GLY* 1.3 59.0 + - - +
148A LEU* 4.7 20.2 - - + -
149A ASN 3.2 11.7 - - - +
150A PHE* 3.6 29.6 - - + -
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Residues in contact with GLY 117 (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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116A LEU* 1.3 76.1 - - - +
118A LEU* 1.4 60.6 + - - -
148A LEU* 3.5 10.5 - - - +
149A ASN* 2.9 38.1 + - - +
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Residues in contact with LEU 118 (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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117A GLY* 1.4 73.1 - - - -
119A ALA* 1.3 76.1 + - - +
120A ALA* 4.2 5.4 - - + +
146A LEU* 4.2 20.0 - - + -
147A THR 3.4 9.9 - - - +
148A LEU* 4.6 6.1 - - + +
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Residues in contact with ALA 119 (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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117A GLY 4.2 0.2 - - - -
118A LEU* 1.3 76.3 - - - +
120A ALA* 1.3 62.1 + - - +
145A THR* 4.6 2.0 - - - +
146A LEU* 3.4 2.6 - - - +
147A THR* 2.8 47.5 + - - +
149A ASN* 3.9 17.7 - - - +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LEU* 4.2 7.0 - - + +
119A ALA* 1.3 77.0 - - - +
121A SER* 1.3 65.5 + - - +
145A THR* 3.2 16.4 - - - +
146A LEU* 3.7 17.9 - - + -
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ALA* 1.3 77.8 - - - +
122A ALA* 1.3 62.2 + - - +
123A THR* 4.4 10.6 + - - -
144A GLY* 3.3 3.7 - - - -
145A THR* 2.6 57.8 + - - +
342A LEU* 4.7 0.3 - - - +
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A SER* 1.3 75.2 - - - +
123A THR* 1.3 63.5 + - - +
143A TYR 3.3 5.8 - - - -
342A LEU* 3.9 27.4 - - + -
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Residues in contact with THR 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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121A SER* 4.4 10.4 + - - -
122A ALA* 1.3 81.1 + - - +
124A GLU* 1.3 73.9 + - - +
125A SER* 4.2 10.8 - - - -
141A ASN 3.5 1.2 - - - +
142A ASP* 3.3 3.1 - - - -
143A TYR* 2.8 49.1 + - - -
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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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123A THR* 1.3 76.1 - - - +
125A SER* 1.3 62.3 + - - +
140A TRP* 3.5 48.1 - - + +
141A ASN* 3.3 17.5 - - - -
142A ASP* 3.3 23.1 + - - +
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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
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123A THR* 4.2 11.9 - - - -
124A GLU* 1.3 76.6 - - - +
126A LYS* 1.3 66.6 + - - +
127A VAL* 4.2 10.6 + - - +
139A GLY 3.5 2.1 - - - +
140A TRP* 4.0 6.1 - - - -
141A ASN* 2.9 31.9 + - - +
143A TYR* 3.8 28.1 + - - -
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Residues in contact with LYS 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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125A SER* 1.3 74.9 + - - +
127A VAL* 1.3 83.7 + - - +
128A SER* 4.1 7.6 + - - +
129A GLU* 4.3 17.3 + - - +
139A GLY* 3.4 31.9 - - - +
140A TRP* 3.5 41.4 - - + +
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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