Contacts of the strand formed by residues 129 - 136 (chain A) in PDB entry 2YWD
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLU* 3.9 9.9 - - - -
125A VAL* 2.8 43.9 + - - +
127A GLY 3.8 0.6 - - - -
128A LEU* 1.3 75.3 - - - +
130A SER* 1.3 65.7 + - - -
131A PHE* 4.4 0.6 - - - +
180A ARG* 4.6 1.1 - - - -
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Residues in contact with SER 130 (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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122A ASP* 4.5 17.2 + - - +
123A LEU 3.2 8.8 + - - -
124A GLU* 3.3 19.5 + - - -
129A GLY* 1.3 69.5 - - - -
131A PHE* 1.3 56.6 + - - +
180A ARG* 2.6 33.8 + - - +
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Residues in contact with PHE 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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122A ASP* 4.6 2.0 - - - -
123A LEU* 2.7 44.0 + - + +
125A VAL* 3.9 22.0 - - + -
128A LEU* 4.2 14.1 - - + -
129A GLY 4.4 0.4 - - - +
130A SER* 1.3 77.0 + - - +
132A HIS* 1.3 79.1 + - - +
133A GLY* 3.3 1.3 + - - -
171A PHE* 4.1 17.9 - + - -
173A PRO* 3.6 37.0 - - + -
176A THR* 3.8 9.2 - - - -
178A ASP* 3.4 49.6 - - + -
180A ARG* 4.2 5.6 - - - +
181A LEU* 3.9 18.2 - - + -
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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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120A GLU* 3.7 34.8 - - + +
121A GLU* 4.0 7.7 + - - -
122A ASP* 3.4 23.3 + - - +
131A PHE* 1.3 90.1 - - + +
133A GLY* 1.3 58.8 + - - +
134A VAL* 3.7 17.5 + - + +
171A PHE* 5.0 0.2 - - - -
176A THR* 3.5 26.0 - - + +
178A ASP* 5.2 3.3 + - + +
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Residues in contact with GLY 133 (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 GLU* 3.2 8.0 - - - +
121A GLU 2.7 45.1 + - - -
123A LEU* 3.9 19.1 - - - -
131A PHE 3.3 3.4 + - - -
132A HIS* 1.3 71.2 - - - +
134A VAL* 1.3 62.3 + - - -
135A PHE* 3.5 8.8 - - - -
171A PHE* 4.2 8.5 - - - -
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Residues in contact with VAL 134 (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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119A PHE 4.0 2.2 - - - -
120A GLU* 4.4 14.4 - - + +
132A HIS* 3.7 25.2 + - + +
133A GLY* 1.3 74.1 - - - +
135A PHE* 1.3 63.6 + - - +
136A ILE* 4.4 13.0 - - + -
171A PHE* 3.3 6.2 - - - +
172A HIS* 2.8 44.7 + - - +
175A LEU* 3.9 33.9 - - + +
176A THR* 3.9 16.8 - - + -
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Residues in contact with PHE 135 (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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112A PHE* 4.3 7.0 - + - -
118A SER* 3.2 3.4 - - - -
119A PHE* 2.8 81.2 + + + +
120A GLU* 4.8 0.5 - - - +
121A GLU* 4.2 14.1 - - + -
123A LEU* 4.1 12.3 - - + -
133A GLY* 3.5 28.0 - - - -
134A VAL* 1.3 72.2 - - - +
136A ILE* 1.3 67.1 + - - +
137A ARG 4.3 0.4 - - - -
138A ALA* 3.7 22.0 - - + -
154A LEU* 4.5 5.2 - - + -
159A VAL* 4.0 16.6 - - + -
170A SER* 3.6 21.5 - - - -
171A PHE* 3.8 25.6 - + + +
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Residues in contact with ILE 136 (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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81A CYS* 4.5 7.4 - - - -
117A GLU 3.5 8.3 - - - +
118A SER* 4.4 10.8 - - - -
134A VAL* 4.2 10.8 + - + -
135A PHE* 1.3 80.3 - - - +
137A ARG* 1.3 102.9 + - - +
138A ALA* 2.9 5.7 + - - +
170A SER 5.2 0.4 + - - -
172A HIS* 4.2 20.2 + - + +
175A LEU* 3.7 29.6 - - + -
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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