Contacts of the strand formed by residues 125 - 132 (chain A) in PDB entry 1YL5
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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A PHE* 3.8 5.8 - - - +
124A ASP* 1.3 80.0 - - - +
126A ALA* 1.3 63.3 + - - +
127A GLU* 5.8 3.4 - - - -
155A ARG* 4.2 2.0 - - - -
161A ASN* 3.7 8.7 - - - -
162A PRO* 3.5 27.2 + - - +
197A LEU 4.4 0.4 - - - -
198A PHE* 3.2 4.9 - - - -
199A GLY* 2.8 39.6 + - - -
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Residues in contact with ALA 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 76.2 - - - +
127A GLU* 1.3 64.5 + - - +
151A ILE* 3.7 32.3 - - + -
155A ARG* 4.1 12.3 - - - +
161A ASN* 2.7 31.8 + - - -
180A ILE* 3.6 6.3 - - + +
181A PRO* 3.5 5.5 - - - +
197A LEU 3.2 5.4 - - - -
198A PHE* 3.7 19.1 - - + -
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Residues in contact with GLU 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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125A SER* 5.7 3.3 - - - -
126A ALA* 1.3 81.7 - - - +
128A VAL* 1.3 64.4 + - - +
129A ILE* 5.7 0.9 - - + -
161A ASN* 4.1 5.0 + - - +
173A ARG* 2.9 29.3 + - - -
180A ILE* 4.1 1.3 - - - -
181A PRO* 3.5 24.6 - - + +
183A HIS* 2.6 36.7 + - + +
195A GLU 4.1 0.2 - - - +
196A VAL* 3.6 6.0 - - - +
197A LEU* 2.9 45.9 + - + +
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Residues in contact with VAL 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 GLU* 1.3 78.3 - - - +
129A ILE* 1.3 66.9 + - - +
144A ALA* 4.1 19.1 - - + -
147A THR* 4.4 9.6 - - + -
148A ALA* 4.4 10.5 - - + +
151A ILE* 4.0 24.7 - - + -
180A ILE* 4.2 9.9 - - + -
181A PRO 2.8 10.7 + - - +
182A VAL* 3.3 10.2 - - + -
183A HIS* 2.9 30.9 + - - -
194A GLN* 3.9 28.7 - - + +
195A GLU 3.5 9.2 - - - +
196A VAL* 4.4 3.1 - - + -
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Residues in contact with ILE 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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127A GLU* 4.2 1.3 - - + -
128A VAL* 1.3 77.7 - - - +
130A GLU* 1.3 64.1 + - - +
131A LEU* 3.2 29.6 - - + +
183A HIS* 3.5 25.4 - - + +
185A VAL* 4.3 8.7 - - + -
194A GLN* 3.5 1.9 - - - +
195A GLU* 2.8 54.3 + - + +
197A LEU* 4.1 30.5 - - + -
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Residues in contact with GLU 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 VAL* 4.7 0.4 - - + -
129A ILE* 1.3 77.1 - - - +
131A LEU* 1.3 63.9 + - - +
132A HIS* 2.6 27.2 + - + +
140A PRO* 3.4 2.1 - - - +
141A SER* 3.1 33.7 + - - +
144A ALA* 3.9 17.7 - - + -
182A VAL* 5.1 0.7 - - + -
183A HIS 2.9 9.5 + - - +
184A ALA* 3.2 12.3 - - - +
185A VAL* 2.8 25.1 + - - +
186A ARG* 2.4 46.6 + - - -
193A HIS 3.6 6.3 - - - +
194A GLN* 4.3 5.8 - - + +
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Residues in contact with LEU 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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129A ILE* 3.2 35.9 - - + +
130A GLU* 1.3 75.1 + - - +
132A HIS* 1.3 63.6 + - - +
185A VAL* 3.2 24.5 - - + -
187A LEU* 5.7 1.8 - - + -
190A LEU* 3.4 29.2 - - + -
193A HIS* 2.7 54.2 + - + -
194A GLN* 6.0 0.2 - - - -
195A GLU* 5.4 4.9 - - + +
208A ARG* 4.3 24.2 - - - +
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Residues in contact with HIS 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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130A GLU* 2.6 39.3 + - + -
131A LEU* 1.3 81.4 + - - +
133A HIS* 1.3 67.4 + + - +
136A LYS* 3.4 32.3 + - + +
141A SER* 3.7 15.0 - - - -
143A THR* 6.4 0.4 - - - -
185A VAL 2.8 6.9 + - - -
186A ARG* 3.1 15.5 - - - +
187A LEU 2.8 30.3 + - - +
190A LEU* 3.9 6.9 - - - +
191A VAL 3.3 19.5 - - - -
192A ALA* 3.5 18.4 - - + +
193A HIS 4.0 7.9 - - - -
194A GLN* 5.9 1.1 - - + -
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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