Contacts of the strand formed by residues 112 - 119 (chain A) in PDB entry 1FE3
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 LYS 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A TRP* 4.3 0.4 - - - -
11A THR* 3.1 28.7 + - - -
12A ASN* 5.5 1.8 - - - +
108A ILE* 3.4 2.2 - - - -
109A LYS 2.7 36.3 + - - +
110A ASP* 3.1 8.9 + - - +
111A GLY* 1.3 79.4 - - - +
113A MET* 1.3 62.6 + - - +
114A VAL* 3.5 3.5 + - + +
127A HIS* 3.5 31.3 - - + +
128A TYR 2.9 25.8 - - - +
129A GLU* 4.2 22.6 - - + +
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Residues in contact with MET 113 (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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4A PHE* 4.5 8.3 - - - -
8A TRP* 3.4 51.0 - - + -
40A VAL* 4.3 13.9 - - + -
42A ILE* 4.1 13.5 - - + -
106A ARG* 3.9 35.9 - - + +
107A GLU 3.2 14.1 - - - +
108A ILE* 3.7 4.0 - - + -
112A LYS* 1.3 70.9 - - - +
114A VAL* 1.3 66.3 + - - +
115A MET* 4.8 0.4 - - + +
127A HIS* 3.6 0.7 - - - -
128A TYR* 2.8 71.6 + - + +
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Residues in contact with VAL 114 (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 VAL 3.6 2.8 - - - +
106A ARG* 3.5 0.3 - - - -
107A GLU* 2.8 61.8 + - + +
109A LYS* 4.1 25.4 - - + +
112A LYS* 3.9 13.2 - - + +
113A MET* 1.3 79.6 - - - +
115A MET* 1.3 62.1 + - - +
116A THR* 4.3 6.1 - - + +
125A VAL* 5.3 3.1 - - + -
126A ARG 3.3 7.2 - - - +
127A HIS* 3.5 33.0 - - + +
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Residues in contact with MET 115 (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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104A PHE* 4.4 12.3 - - + -
105A VAL 3.7 4.7 - - - +
106A ARG* 3.6 46.4 - - + +
113A MET* 4.1 1.4 + - + -
114A VAL* 1.3 73.8 - - - +
116A THR* 1.3 66.4 + - - +
117A LEU* 3.6 33.7 - - + -
125A VAL* 3.5 3.5 - - - +
126A ARG* 2.8 47.6 + - + +
128A TYR* 3.6 32.3 - - + +
133A OLA 3.7 19.7 - - + -
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Residues in contact with THR 116 (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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103A ASN 3.9 0.2 - - - +
105A VAL* 3.3 41.6 + - + +
107A GLU* 4.1 16.2 - - - +
114A VAL* 4.3 8.1 - - + +
115A MET* 1.3 80.8 - - - +
117A LEU* 1.3 60.8 + - - +
118A THR* 3.7 10.7 - - - +
123A VAL* 4.3 11.1 - - - +
124A ALA 3.3 6.3 - - - -
125A VAL* 3.8 20.9 - - + -
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Residues in contact with LEU 117 (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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16A PHE* 3.8 18.8 - - + -
19A TYR* 3.6 23.1 - - + -
103A ASN 3.9 4.9 - - - -
104A PHE* 3.3 26.7 - - + -
115A MET* 3.6 28.9 - - + -
116A THR* 1.3 72.3 - - - +
118A THR* 1.3 60.8 + - - +
123A VAL* 3.4 2.3 - - - +
124A ALA* 2.6 55.3 + - + +
125A VAL* 4.4 0.7 - - - -
126A ARG* 3.2 35.4 - - + -
133A OLA 4.8 5.4 - - + -
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Residues in contact with THR 118 (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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19A TYR* 3.4 5.8 - - - -
102A THR* 2.8 22.0 + - - -
103A ASN* 3.1 56.6 + - - +
105A VAL* 5.2 1.8 - - + -
116A THR* 3.7 11.0 - - - +
117A LEU* 1.3 78.1 - - - +
119A PHE* 1.3 63.0 + - - +
120A GLY 4.4 8.0 + - - -
122A VAL 3.9 4.1 + - - -
123A VAL* 4.1 18.0 - - - +
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Residues in contact with PHE 119 (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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19A TYR* 3.7 16.4 - - + -
22A ALA* 3.7 31.0 - - + -
23A LEU* 3.6 23.1 - - + -
97A TRP* 3.6 19.1 - + - -
100A LYS* 4.1 26.0 - - + -
101A GLU 3.0 31.0 - - - -
102A THR* 3.8 4.5 - - - +
118A THR* 1.3 77.0 + - - +
120A GLY* 1.3 73.8 + - - +
122A VAL* 2.9 38.5 + - + +
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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