Contacts of the strand formed by residues 113 - 118 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B GLU* 3.4 26.2 - - - -
30B LEU* 4.0 21.7 - - + +
33B LEU* 3.9 24.2 - - + -
90B ALA* 3.1 16.5 + - + +
91B THR* 3.3 8.6 - - + -
92B CYS* 2.9 25.3 + - - -
93B VAL 3.6 1.2 + - - -
111B GLY 3.4 1.4 + - - -
112B LYS* 1.3 90.4 - - + +
114B VAL* 1.3 64.0 + - - +
115B VAL 4.1 0.2 - - - -
138B ILE* 3.7 19.3 - - + -
139B TYR 3.7 9.6 - - - +
140B ARG* 4.0 17.3 - - + -
160B VAL* 4.2 9.9 - - + -
338B AMP 2.8 58.5 + - - -
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B CYS* 3.8 18.2 - - - -
93B VAL* 3.2 27.6 - - + +
95B VAL* 5.4 0.4 - - + -
113B TYR* 1.3 76.9 - - - +
115B VAL* 1.3 60.0 + - - +
116B CYS* 4.6 5.6 - - - -
137B GLY 3.7 0.7 - - - +
138B ILE* 3.2 4.3 - - - -
139B TYR* 2.8 54.8 + - + +
141B LYS* 3.8 18.6 - - + -
151B ASP* 4.1 22.7 - - + +
152B ALA* 4.1 16.2 - - + -
154B GLN* 4.4 0.7 - - - +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 4.1 16.4 - - + -
37B LEU* 4.8 7.0 - - + -
85B LEU* 3.9 11.7 - - + -
91B THR* 3.9 23.3 - - + -
93B VAL 3.1 5.9 + - - +
94B LEU* 3.4 15.3 - - + -
95B VAL 3.0 23.2 + - - +
114B VAL* 1.3 77.0 - - - +
116B CYS* 1.3 67.1 + - - +
117B PHE* 3.7 22.9 - - + -
136B PHE* 4.7 7.2 - - + -
137B GLY 3.2 8.7 - - - +
138B ILE* 4.0 20.4 - - + -
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Residues in contact with CYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B VAL* 3.2 28.9 - - + +
114B VAL* 4.6 7.4 - - - -
115B VAL* 1.3 75.7 - - - +
117B PHE* 1.3 59.6 + - - +
136B PHE* 3.3 2.3 - - - +
137B GLY 2.8 33.5 + - - +
139B TYR* 3.8 28.5 - - + -
152B ALA* 4.6 1.3 - - - -
278B LEU* 3.7 36.6 - - + +
279B TYR* 3.9 11.1 - - + +
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 6.2 0.7 - - + -
78B ASN* 3.7 19.5 - - - -
81B VAL* 3.8 28.7 - - + -
82B MET* 3.7 25.6 - - + -
85B LEU* 4.0 15.9 - - + -
94B LEU* 4.4 9.0 - - + -
95B VAL 3.0 15.3 + - - +
96B SER* 3.6 12.2 - - - -
97B GLU 3.5 19.1 + - - -
115B VAL* 3.7 25.4 - - + -
116B CYS* 1.3 74.2 - - - +
118B ASP* 1.3 60.0 + - - +
119B PRO* 3.7 19.0 - - + +
134B THR* 5.4 3.1 - - + -
135B ILE 3.1 14.6 - - - +
136B PHE* 4.0 10.5 - - + -
279B TYR* 3.7 9.2 - - - +
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU* 3.7 25.6 - - - +
117B PHE* 1.3 73.1 - - - +
119B PRO* 1.3 69.7 - - - +
120B LEU 3.3 3.8 + - - +
121B ASP* 3.2 27.6 + - - +
133B GLY 4.0 1.6 - - - +
134B THR* 3.5 1.9 - - - +
135B ILE* 3.0 33.8 + - + +
276B ARG* 4.0 3.1 + - - -
279B TYR* 3.8 21.2 - - + +
280B GLU* 3.0 30.8 - - - +
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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