Contacts of the strand formed by residues 113 - 118 (chain D) in PDB entry 1FTA
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 TYR 113 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D GLU* 3.4 23.1 - - - -
30D LEU* 4.1 23.3 - - + -
33D LEU* 3.6 27.4 - - + -
90D ALA* 2.9 17.0 + - + +
91D THR* 3.0 10.8 - - - -
92D CYS* 2.9 28.4 + - - -
93D VAL 3.9 0.2 + - - -
111D GLY 3.5 1.2 - - - -
112D LYS* 1.3 87.1 - - + +
114D VAL* 1.3 62.1 + - - +
115D VAL* 4.0 0.7 - - - -
138D ILE* 3.9 11.2 - - + -
139D TYR 3.1 20.4 - - - +
140D ARG* 3.9 19.9 + - + -
160D VAL* 4.2 9.0 - - + -
338D AMP 2.5 53.6 + - - -
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D CYS* 4.4 8.5 - - - -
93D VAL* 3.2 27.4 - - + +
95D VAL* 5.1 0.2 - - + -
113D TYR* 1.3 74.1 - - - +
115D VAL* 1.3 63.2 + - - +
116D CYS* 4.4 9.0 - - - -
137D GLY 3.9 0.5 - - - +
138D ILE* 3.4 2.8 - - - +
139D TYR* 2.7 49.9 + - + +
141D LYS* 4.6 12.3 - - + +
151D ASP* 3.9 30.3 - - + +
152D ALA* 3.7 32.3 - - + -
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 4.2 16.2 - - + -
37D LEU* 5.4 2.7 - - + -
81D VAL* 6.1 0.2 - - + -
85D LEU* 4.1 19.3 - - + -
91D THR* 3.5 31.4 - - + -
93D VAL 3.1 5.9 + - - +
94D LEU* 3.4 14.0 - - + -
95D VAL 2.9 24.9 + - - +
113D TYR 4.4 0.9 - - - +
114D VAL* 1.3 78.6 - - - +
116D CYS* 1.3 68.3 + - - +
117D PHE* 4.2 8.7 - - + -
136D PHE* 4.7 9.6 - - + -
137D GLY 3.6 9.6 - - - +
138D ILE* 4.0 14.8 - - + -
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Residues in contact with CYS 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D VAL* 3.4 22.9 - - + +
114D VAL* 4.4 2.0 - - - -
115D VAL* 1.3 77.8 - - - +
117D PHE* 1.3 60.9 + - - +
136D PHE* 3.3 3.3 - - - +
137D GLY* 3.0 34.3 + - - +
139D TYR* 4.1 27.4 - - + -
152D ALA* 4.2 16.6 - - - -
278D LEU* 3.4 35.5 - - + +
279D TYR* 4.0 6.9 - - + +
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Residues in contact with PHE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ASN* 3.5 18.6 - - - -
81D VAL* 3.6 41.7 - - + -
82D MET* 3.8 31.2 - - - -
85D LEU* 4.3 6.7 - - + -
94D LEU* 4.3 14.6 - - + -
95D VAL 2.9 18.3 + - - +
96D SER* 3.5 11.7 - - - -
97D GLU 3.1 23.4 + - - -
115D VAL* 4.2 13.9 - - + -
116D CYS* 1.3 76.5 - - - +
118D ASP* 1.3 59.2 + - - +
119D PRO* 3.7 18.8 - - + +
134D THR* 5.6 2.7 - - + -
135D ILE 3.1 13.5 - - - +
136D PHE* 4.1 10.1 - - + -
279D TYR* 3.8 9.0 - - - +
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Residues in contact with ASP 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D GLU* 3.8 24.5 - - - +
117D PHE* 1.3 73.0 - - - +
119D PRO* 1.3 70.7 - - - +
120D LEU 3.4 3.8 + - - +
121D ASP* 2.8 45.1 + - - +
134D THR* 3.5 2.1 - - - +
135D ILE* 2.9 34.2 + - + +
276D ARG* 5.0 0.2 + - - -
279D TYR* 3.7 23.6 - - + +
280D GLU* 3.3 10.3 - - - +
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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