Contacts of the strand formed by residues 131 - 136 (chain A) in PDB entry 4RWN
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 LEU 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ILE* 3.9 28.9 - - + +
99A GLN* 5.7 0.4 - - - +
101A ILE* 3.7 31.2 - - + -
102A ARG* 3.8 29.8 - - + +
105A LEU* 4.0 6.1 - - + -
118A PHE* 3.8 35.9 - - + -
130A ALA* 1.3 71.8 - - - +
132A SER* 1.3 59.6 + - - +
133A PHE* 3.5 14.7 - - + -
146A PHE 3.8 0.5 - - - +
148A VAL* 2.8 38.1 + - + +
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Residues in contact with SER 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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118A PHE* 3.6 5.9 - - - -
119A GLU* 3.1 48.7 + - - +
130A ALA* 3.9 11.6 + - - +
131A LEU* 1.3 74.1 - - - +
133A PHE* 1.3 64.6 + - - +
146A PHE 3.2 5.6 - - - -
147A ASP* 2.8 23.2 + - - -
402A APC 5.1 3.1 - - - -
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Residues in contact with PHE 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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36A VAL* 4.5 13.5 - - + -
105A LEU* 3.9 20.0 - - + -
116A VAL* 4.1 22.9 - - + -
117A THR 3.1 15.7 - - - +
118A PHE* 3.7 20.0 - + + -
119A GLU* 3.9 5.3 + - - -
131A LEU* 3.5 31.2 - - + -
132A SER* 1.3 74.9 - - - +
134A VAL* 1.3 69.2 + - - +
135A LEU* 4.5 7.9 - - + -
145A GLU* 3.4 2.9 - - - +
146A PHE* 2.7 66.7 + + + +
148A VAL* 3.7 21.8 - - + -
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Residues in contact with VAL 134 (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 LYS 3.6 0.9 - - - +
116A VAL* 3.3 6.2 - - - -
117A THR* 2.7 47.2 + - + +
119A GLU* 5.0 8.7 - - - +
133A PHE* 1.3 78.1 - - - +
135A LEU* 1.3 63.9 + - - +
136A SER* 4.0 2.5 + - - +
143A GLU* 3.4 44.9 - - + +
144A VAL 3.6 5.2 - - - +
145A GLU* 4.3 15.3 - - + -
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Residues in contact with LEU 135 (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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32A ALA* 4.6 3.8 - - + -
35A ILE* 4.6 12.8 - - + -
36A VAL* 4.6 11.0 - - + -
105A LEU* 5.8 0.7 - - + -
114A PHE* 3.7 20.9 - - + -
115A LYS 3.5 12.6 - - - +
116A VAL* 3.6 20.6 - - + -
133A PHE* 4.2 6.3 + - + -
134A VAL* 1.3 73.1 - - - +
136A SER* 1.3 69.5 + - - +
137A SER* 4.2 6.1 - - - -
140A LEU* 3.7 25.9 - - + +
142A GLN 4.3 2.1 - - - +
143A GLU* 3.4 6.6 - - - -
144A VAL* 2.8 37.4 + - + +
146A PHE* 3.7 21.5 - - + -
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Residues in contact with SER 136 (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* 3.2 7.3 - - - +
115A LYS* 2.8 61.1 + - - -
134A VAL* 4.5 2.9 + - - +
135A LEU* 1.3 76.7 - - - +
137A SER* 1.3 62.6 + - - +
140A LEU* 5.0 0.9 - - - -
142A GLN 5.3 1.3 - - - -
143A GLU* 3.3 30.7 + - - +
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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