Contacts of the strand formed by residues 125 - 130 (chain J) in PDB entry 3FFC
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 THR 125 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6J GLN* 3.6 11.5 + - - +
7J SER 4.0 3.5 + - - -
8J PRO* 2.6 38.9 + - + +
9J ARG 3.3 8.3 - - - +
10J TYR 4.4 2.7 - - - +
11J LYS* 4.6 1.1 - - + +
21J PHE* 3.4 40.3 - - + +
100J ALA 3.8 0.2 - - - +
101J VAL* 3.2 5.4 - - - +
102J TYR* 2.8 36.0 + - - -
124J GLY* 1.3 73.8 - - - -
126J ARG* 1.3 69.6 + - - +
127J LEU 3.5 1.6 + - - -
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Residues in contact with ARG 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ARG 2.7 10.7 + - - +
10J TYR* 3.3 26.1 - - + -
11J LYS 2.9 27.2 + - - +
46J LEU* 5.4 10.5 - - - +
100J ALA* 3.9 5.7 + - - +
101J VAL* 3.9 22.6 - - + +
124J GLY 4.1 0.6 - - - -
125J THR* 1.3 69.6 - - - +
127J LEU* 1.3 61.5 + - - +
128J THR* 3.9 15.9 + - - +
168J PRO* 5.7 0.4 - - - +
169J ASP* 3.1 43.6 + - - +
170J HIS* 3.4 21.3 + - + -
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Residues in contact with LEU 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J LYS* 3.5 20.4 - - + +
13J ILE* 3.7 24.2 - - + -
19J VAL* 3.8 30.5 - - + -
21J PHE* 3.8 28.0 - - + -
91J ILE* 4.2 7.2 - - + -
98J ASP* 4.0 6.3 - - + +
99J SER* 3.2 5.0 - - - -
100J ALA 2.9 35.1 + - - +
102J TYR* 3.9 14.4 - - + -
125J THR 3.5 1.4 + - - -
126J ARG* 1.3 75.4 + - - +
128J THR* 1.3 64.6 + - - +
129J VAL* 3.7 22.2 - - + -
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Residues in contact with THR 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J LYS 3.0 7.4 + - - -
12J ILE* 3.4 6.0 - - + +
13J ILE 3.1 24.6 + - - +
99J SER* 3.6 6.2 - - - +
126J ARG* 3.9 13.8 + - - +
127J LEU* 1.3 74.8 + - - +
129J VAL* 1.3 61.0 + - - +
130J LEU* 3.6 28.4 + - + -
168J PRO* 3.7 20.0 - - + +
170J HIS* 2.7 34.3 - - - -
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Residues in contact with VAL 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J ILE* 3.3 20.4 - - + +
15J LYS* 3.9 25.1 - - - +
94J ALA* 4.3 2.0 - - + -
95J LYS 3.5 26.7 - - - +
96J LEU* 3.3 30.8 - - + +
98J ASP* 4.1 2.2 - - + -
99J SER* 2.7 26.2 + - - +
127J LEU* 3.7 30.7 - - + -
128J THR* 1.3 71.5 - - - +
130J LEU* 1.3 63.2 + - - +
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Residues in contact with LEU 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J ILE* 3.7 13.9 - - + -
13J ILE 2.9 10.1 + - - +
14J GLU* 3.4 2.8 - - - -
15J LYS* 2.7 34.0 + - - +
96J LEU* 4.6 1.3 - - - -
128J THR* 3.6 26.9 - - + -
129J VAL* 1.3 76.3 - - - +
131J GLU* 1.3 60.4 + - - +
132J ASP 3.9 21.5 - - - +
133J LEU* 4.4 3.8 - - + -
135J ASN* 5.1 1.6 - - + +
136J VAL* 3.4 33.9 - - + +
167J TYR* 3.5 38.6 - - + +
168J PRO* 4.6 1.8 - - + -
201J ASP* 5.9 0.4 - - + -
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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