Contacts of the strand formed by residues 126 - 133 (chain A) in PDB entry 3SJ5
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 ALA 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PRO* 3.6 4.0 - - - +
122A VAL* 3.0 25.6 + - + -
123A ALA* 3.3 9.3 + - + +
124A LYS 3.7 0.2 - - - -
125A ASP* 1.3 86.6 - - - +
127A ILE* 1.3 64.5 + - - +
175A ARG* 3.8 39.0 - - - +
176A ILE 3.1 14.1 - - - +
177A LYS* 3.9 3.4 - - - -
178A PHE* 4.2 3.1 - - - -
183A PHE* 3.6 4.4 - - - -
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 4.3 0.9 - - + -
95A LEU* 4.3 20.0 - - + -
96A MET* 4.1 14.1 - - + -
119A ALA* 4.0 21.3 - - + -
120A LYS 3.2 14.6 - - - +
122A VAL* 4.0 5.6 - - - -
126A ALA* 1.3 72.3 - - - +
128A GLU* 1.3 59.3 + - - +
129A MET* 4.6 2.9 - - + -
175A ARG* 3.4 4.7 - - - +
176A ILE* 2.8 63.8 + - + -
178A PHE* 4.0 16.6 - - + -
183A PHE* 3.3 36.3 - - + -
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Residues in contact with GLU 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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118A ILE 4.0 1.1 - - - +
119A ALA* 3.2 3.6 - - - +
120A LYS* 2.9 53.9 + - - +
122A VAL* 3.7 25.1 - - + +
127A ILE* 1.3 76.7 - - - +
129A MET* 1.3 60.1 + - - +
161A VAL* 4.4 13.7 - - + +
173A LYS* 3.7 28.4 + - + +
174A VAL 3.2 12.3 - - - +
175A ARG* 4.3 15.6 - - + +
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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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95A LEU* 3.8 30.3 - - + +
98A MET* 4.1 5.8 - - + -
117A LEU* 3.4 42.4 - - + +
118A ILE 3.3 4.3 - - - +
119A ALA* 4.1 8.7 - - + -
127A ILE* 4.2 2.4 + - + -
128A GLU* 1.3 75.2 - - - +
130A GLU* 1.3 62.7 + - - +
141A PHE* 4.3 14.0 - - + -
145A ILE* 4.5 1.3 - - - -
172A LEU 3.8 1.2 - - - +
173A LYS* 3.5 2.8 - - - -
174A VAL* 2.9 43.5 + - + +
176A ILE* 4.4 19.3 - - + -
500A HEM 3.6 29.6 - - + -
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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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116A ARG* 3.2 12.8 - - - +
117A LEU* 3.5 11.9 - - - -
118A ILE* 2.9 19.8 + - + +
129A MET* 1.3 74.4 - - - +
131A TYR* 1.3 69.8 + - - +
132A VAL* 3.7 8.1 + - + +
141A PHE* 4.7 1.6 - - - -
162A GLU* 4.6 4.5 - - - +
171A ARG* 2.8 51.1 + - - +
172A LEU 3.4 9.0 - - - +
173A LYS* 3.9 35.3 + - + +
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Residues in contact with TYR 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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115A PRO* 3.9 5.2 - - + -
116A ARG 3.5 3.1 - - - -
117A LEU* 4.0 7.9 - - + -
130A GLU* 1.3 71.0 - - - +
132A VAL* 1.3 64.0 + - - +
133A SER* 3.2 28.3 + - - -
136A LYS* 3.5 6.0 + - - -
137A MET 2.8 32.6 + - - -
138A TYR* 4.0 29.8 - + - -
141A PHE* 3.7 44.5 - + + -
170A SER* 4.4 3.4 - - - -
171A ARG* 3.1 6.4 - - - -
172A LEU* 2.8 41.1 + - + +
500A HEM 2.6 44.3 + - + -
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Residues in contact with VAL 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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114A PRO 4.6 0.5 - - - +
115A PRO* 3.6 1.3 - - - +
116A ARG* 2.9 50.6 + - + +
118A ILE* 6.5 0.9 - - + -
130A GLU* 3.8 33.0 - - + +
131A TYR* 1.3 80.5 - - - +
133A SER* 1.3 64.2 + - - +
169A PHE* 4.0 23.4 - - + -
170A SER 3.3 7.6 - - - +
171A ARG* 3.8 26.9 - - + +
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Residues in contact with SER 133 (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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113A THR 5.0 1.9 + - - -
114A PRO 5.6 0.9 - - - -
115A PRO* 4.2 6.3 - - - +
131A TYR* 3.2 29.5 - - - -
132A VAL* 1.3 77.4 - - - +
134A LYS* 1.3 61.7 + - - +
135A ARG* 3.1 12.6 + - - +
169A PHE* 4.1 8.7 - - - -
170A SER* 2.7 42.0 + - - -
500A HEM 2.6 25.2 + - - -
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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