Contacts of the strand formed by residues 126 - 132 (chain A) in PDB entry 5T5W
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A VAL* 4.5 1.2 - - - -
123A LEU* 2.3 57.6 + - - +
124A ALA 3.6 4.5 - - - +
125A ASP* 1.3 84.3 + - - +
127A LEU* 1.3 66.6 + - - +
128A HIS* 3.5 11.7 + - - -
177A VAL* 5.5 1.3 - - - -
178A LEU 3.2 11.4 - - - -
179A ARG* 4.3 19.7 - - - +
212A THR* 4.3 6.1 - - - +
117B GLU* 5.2 3.1 + - - -
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Residues in contact with LEU 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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120A VAL* 3.6 30.5 - - + -
121A GLU 3.6 6.7 - - - +
122A VAL* 5.2 4.0 - - + -
126A SER* 1.3 78.0 - - - +
128A HIS* 1.3 64.0 + - - +
129A MET* 3.7 24.3 + - - +
176A GLU 3.9 0.3 - - - +
177A VAL* 3.6 2.5 - - - -
178A LEU* 3.0 35.1 + - + +
181A LEU* 3.9 25.4 - - + -
187A TYR* 4.6 13.7 - - + +
189A VAL* 4.4 11.9 - - + -
210A GLU* 4.6 17.9 - - + +
212A THR* 4.3 15.5 - - + -
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Residues in contact with HIS 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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119A GLN 3.8 0.7 - - - +
120A VAL* 3.3 2.1 - - - +
121A GLU* 2.6 47.5 + - + +
123A LEU* 3.5 33.3 - - + +
126A SER* 3.5 15.9 + - - -
127A LEU* 1.3 72.5 - - - +
129A MET* 1.3 59.4 + - - +
130A ARG 4.3 0.2 - - - -
175A PHE* 3.6 11.6 - - + -
176A GLU 3.7 5.4 - - - -
177A VAL* 3.5 18.9 - - + +
117B GLU* 3.7 18.4 + - + +
118B ILE* 3.4 22.6 - - + +
165B THR* 2.9 36.8 + - + +
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Residues in contact with MET 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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118A MET* 4.3 4.9 - - + +
119A GLN 3.1 7.4 - - - +
120A VAL* 3.9 13.5 - - + -
127A LEU* 4.0 21.5 - - + +
128A HIS* 1.3 75.7 - - - +
130A ARG* 1.3 60.7 + - - +
131A PHE* 3.9 18.0 - - + -
156A VAL* 3.6 29.6 - - + -
169A ILE* 3.7 8.7 - - + -
175A PHE* 3.8 5.7 - - - -
176A GLU* 3.1 43.1 + - + +
178A LEU* 3.6 30.5 - - + +
189A VAL* 4.2 17.7 - - - -
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Residues in contact with ARG 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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118A MET* 3.2 5.4 - - - +
119A GLN* 2.7 58.4 + - + +
129A MET* 1.3 72.6 - - - +
131A PHE* 1.3 72.2 + - - +
132A LEU* 4.1 5.1 + - + +
174A ASP* 3.5 17.6 + - + +
175A PHE* 3.5 30.2 - - + +
153B PHE* 3.8 32.0 - - - -
154B PRO* 3.7 30.9 - - + +
162B VAL* 4.5 9.7 - - - +
163B GLN 2.5 32.5 + - - +
164B ILE* 4.1 3.4 - - - +
165B THR* 4.6 2.6 + - - +
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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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117A GLY 3.4 5.8 - - - +
118A MET* 4.5 6.1 - - + -
129A MET* 3.9 30.1 - - + -
130A ARG* 1.3 78.9 - - - +
132A LEU* 1.3 66.0 + - - +
133A ALA 4.1 1.2 + - - -
154A TYR* 3.9 30.7 + + + -
156A VAL* 3.5 29.4 - - + -
171A PRO* 3.6 25.4 - - + -
173A TYR 3.9 2.9 - - - -
174A ASP* 3.0 56.2 + - - +
175A PHE* 3.8 7.4 - - - -
176A GLU* 3.9 8.3 - - + -
191A VAL* 3.6 24.9 - - + -
154B PRO* 5.2 3.8 - - - +
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Residues in contact with LEU 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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116A PRO* 3.1 8.7 - - - +
117A GLY* 2.8 50.7 + - - +
118A MET 4.3 1.1 - - - +
119A GLN* 3.6 40.2 - - + +
130A ARG* 4.4 5.8 - - + +
131A PHE* 1.3 77.1 - - - +
133A ALA* 1.3 65.5 + - - +
154A TYR* 3.8 1.6 - - - -
154B PRO* 3.7 32.1 - - + -
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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