Contacts of the strand formed by residues 125 - 130 (chain A) in PDB entry 1F6A
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 GLU 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR* 3.2 10.1 - - - -
122A LYS* 2.9 39.5 + - + +
123A ASP* 2.9 14.9 + - - +
124A GLY* 1.3 80.7 - - - +
126A ALA* 1.3 62.6 + - - +
127A LEU* 3.2 2.1 + - - -
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Residues in contact with ALA 126 (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 ILE* 4.6 4.9 - - + -
120A TYR 4.1 1.6 - - - -
121A TYR* 3.7 18.0 - - + -
124A GLY 4.2 0.2 + - - -
125A GLU* 1.3 72.8 - - - +
127A LEU* 1.3 64.9 + - - +
128A LYS 3.8 0.2 - - - -
393B ARG 3.5 25.4 + - - +
394B ASN 3.9 4.7 - - - +
395B GLY* 3.5 23.7 - - - +
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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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105A LEU* 5.4 0.2 - - + -
120A TYR* 2.9 25.8 + - + +
122A LYS* 3.7 27.8 - - + +
125A GLU* 3.2 3.6 + - - -
126A ALA* 1.3 75.1 - - - +
128A LYS* 1.3 64.3 + - + +
136A ILE* 5.4 12.8 - - + -
138A ILE* 5.9 2.5 - - + -
145A ASP* 5.8 1.1 - - - +
149A TYR* 3.5 33.4 - - + +
395B GLY* 6.4 0.2 - - - -
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Residues in contact with LYS 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 VAL 3.8 1.2 - - - +
119A ILE* 3.3 4.8 - - - -
120A TYR* 3.0 27.1 + - - +
126A ALA 3.8 0.8 - - - -
127A LEU* 1.3 85.6 - - + +
129A TYR* 1.3 68.7 + - - +
130A TRP* 6.2 4.0 - - - -
134A HIS* 4.0 20.1 + - + +
136A ILE* 4.1 27.8 - - + -
395B GLY* 5.9 1.6 - - - -
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Residues in contact with TYR 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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117A LYS* 3.7 30.8 - - + +
118A VAL 3.5 5.6 - - - -
119A ILE* 3.5 35.0 - - + -
128A LYS* 1.3 82.2 - - - +
130A TRP* 1.3 88.0 + - - +
131A TYR* 4.0 11.2 - + - -
134A HIS* 4.4 1.3 - - - -
362B ASP* 2.8 40.3 + - + +
363B LEU 4.0 4.9 - - - -
364B ALA* 3.8 28.2 - - + +
365B PRO* 5.1 5.3 - - + +
394B ASN 4.8 1.1 - - - -
395B GLY* 4.1 25.1 + - - +
396B THR* 4.6 4.7 - - - -
1G NAG 4.5 10.3 - - + -
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Residues in contact with TRP 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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117A LYS* 3.3 18.9 - - - -
118A VAL 3.3 9.1 + - - -
128A LYS* 5.7 4.3 - - + -
129A TYR* 1.3 90.5 - - - +
131A TYR* 1.3 94.9 + + - +
132A GLU* 3.0 41.4 + - + +
133A ASN 4.1 6.3 - - - -
134A HIS* 3.4 33.0 - + + +
201B SO4 3.4 25.2 + - - -
202B SO4 5.6 0.4 - - - -
334B ARG* 3.4 26.4 - - - +
364B ALA* 4.2 6.7 - - + -
365B PRO 5.4 1.3 - - - -
424B HIS* 3.9 22.7 - + - -
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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