Contacts of the strand formed by residues 136 - 143 (chain A) in PDB entry 3FPK
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 ASN 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A GLU* 2.9 19.2 + - - +
108A THR* 3.0 23.8 + - + +
109A LEU 3.0 24.0 + - - -
134A PHE* 3.9 2.6 - - - +
135A LYS* 1.3 101.5 + - - +
137A LEU* 1.3 67.5 + - - +
165A LYS* 3.9 9.3 + - - +
167A ARG* 4.7 9.5 - - - +
200A LEU* 3.5 41.3 - - + +
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Residues in contact with LEU 137 (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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109A LEU* 3.5 19.5 - - + -
111A MET* 4.0 8.5 - - + -
125A LEU* 3.9 13.9 - - + -
131A VAL* 4.3 13.9 - - + -
134A PHE* 3.9 28.7 - - + -
136A ASN* 1.3 79.9 - - - +
138A VAL* 1.3 67.4 + - - +
162A TYR* 3.7 34.8 - - + -
165A LYS* 3.1 27.3 + - + +
166A LEU* 3.7 15.3 - - + -
167A ARG* 2.9 25.6 + - - +
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Residues in contact with VAL 138 (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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108A THR* 3.8 24.2 - - + -
109A LEU 2.8 11.4 + - - +
110A TRP* 3.6 35.9 - - + -
111A MET* 2.7 38.0 + - - +
137A LEU* 1.3 79.9 - - - +
139A LEU* 1.3 59.4 + - - +
140A VAL* 4.1 8.9 - - + +
167A ARG* 3.2 11.2 - - + +
198A VAL* 3.7 34.3 - - + -
200A LEU* 3.8 9.6 - - + -
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Residues in contact with LEU 139 (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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111A MET* 3.5 7.2 - - + +
118A ILE* 3.4 27.1 - - + -
121A TYR* 3.6 32.3 - - + -
122A LEU* 4.4 9.0 - - + -
125A LEU* 3.9 18.8 - - + -
138A VAL* 1.3 72.6 - - - +
140A VAL* 1.3 61.8 + - - +
155A MET* 4.0 32.5 - - + -
158A LEU* 5.4 1.8 - - + -
166A LEU* 4.1 14.2 - - + +
167A ARG 2.8 10.1 + - - +
168A ILE* 3.2 19.0 - - + +
169A GLN 2.8 25.8 + - - -
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Residues in contact with VAL 140 (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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110A TRP* 4.3 2.7 - - + -
111A MET 2.8 10.9 + - - +
112A LEU* 3.7 30.3 - - + -
113A ALA* 3.0 28.6 + - - +
118A ILE* 4.5 3.1 - - - +
138A VAL* 4.1 17.9 - - + -
139A LEU* 1.3 77.6 - - - +
141A HIS* 1.3 62.1 + - - +
142A ALA 4.8 0.2 - - - +
169A GLN* 3.2 12.3 - - + +
171A VAL* 3.9 22.9 - - + -
185A VAL* 4.7 10.5 - - + -
194A LEU* 4.1 26.7 - - + -
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Residues in contact with HIS 141 (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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66A TYR* 4.4 13.7 - + - -
113A ALA 3.9 7.0 - - - -
115A GLY* 2.9 31.7 + - - -
118A ILE* 3.8 36.0 - - + +
139A LEU* 4.1 1.2 - - - +
140A VAL* 1.3 73.0 - - - +
142A ALA* 1.3 72.9 + - - +
143A ALA* 4.2 2.4 - - - +
148A ASP 4.4 2.0 - - - -
149A LEU* 3.8 31.7 - - + +
150A SER 4.6 2.5 - - - -
151A TYR* 5.3 2.7 + + - -
155A MET* 3.8 23.6 - - + +
168A ILE* 5.7 0.6 - - + +
169A GLN 3.0 8.3 + - - +
170A THR* 3.2 9.2 - - + -
171A VAL 2.8 25.5 + - - +
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Residues in contact with ALA 142 (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 ALA 2.9 12.3 + - - +
114A THR* 3.2 13.6 - - + -
115A GLY 2.8 31.5 + - - -
140A VAL 4.0 0.8 - - - -
141A HIS* 1.3 74.7 - - - +
143A ALA* 1.3 54.3 + - - +
171A VAL* 3.3 18.2 - - + +
183A GLY 5.7 0.4 - - - +
185A VAL* 3.7 30.7 - - + +
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Residues in contact with ALA 143 (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 GLY* 4.4 12.6 - - - +
141A HIS* 4.2 4.4 + - - +
142A ALA* 1.3 75.4 - - - +
144A ARG* 1.3 67.7 + - - +
145A PHE 3.5 1.8 - - - +
148A ASP* 3.6 29.6 - - + +
149A LEU* 3.9 18.4 - - + +
171A VAL 3.0 6.4 + - - -
172A VAL* 3.3 17.8 - - - -
173A SER* 3.4 5.0 + - - -
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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