Contacts of the strand formed by residues 113 - 118 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C GLU* 3.8 8.3 - - + -
30C LEU* 3.8 24.1 - - + +
33C LEU* 3.5 26.5 - - + -
90C ALA 3.0 16.9 + - - +
91C THR* 3.3 6.5 - - - -
92C CYS* 2.9 26.3 + - - -
93C VAL 3.9 0.2 + - - -
112C LYS* 1.3 98.2 - - + +
114C VAL* 1.3 61.3 + - - +
115C VAL* 4.9 0.2 - - - -
138C ILE* 3.7 11.9 - - + -
139C TYR 3.2 16.2 - - - +
140C ARG* 4.2 15.8 - - + -
160C VAL* 4.4 7.0 - - + -
338C AMP 2.9 65.4 + - - -
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C CYS* 4.0 15.5 - - - -
93C VAL* 3.3 23.1 - - + +
95C VAL* 5.8 0.2 - - + -
113C TYR* 1.3 77.3 - - - +
115C VAL* 1.3 59.6 + - - +
116C CYS* 4.9 2.7 - - - -
138C ILE* 3.6 1.4 - - - -
139C TYR* 2.8 48.9 + - + +
140C ARG 4.6 0.7 - - - -
141C LYS* 4.0 15.9 - - - +
151C ASP* 3.8 25.6 - - + +
152C ALA* 3.7 30.3 - - + +
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Residues in contact with VAL 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.0 30.1 - - + -
37C LEU* 5.6 3.4 - - + -
85C LEU* 4.1 16.8 - - + -
91C THR* 4.1 15.3 - - + -
93C VAL 3.1 7.5 + - - +
94C LEU* 3.4 14.1 - - + -
95C VAL 2.8 23.9 + - - +
114C VAL* 1.3 76.9 - - - +
116C CYS* 1.3 70.8 + - - +
117C PHE* 4.1 11.3 - - + -
136C PHE* 4.6 7.6 - - + -
137C GLY 3.4 12.3 - - - +
138C ILE* 4.1 15.9 - - + -
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Residues in contact with CYS 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C VAL* 3.2 21.3 - - + +
114C VAL* 4.9 1.6 - - - -
115C VAL* 1.3 77.5 - - - +
117C PHE* 1.3 61.1 + - - +
136C PHE* 3.4 1.0 - - - +
137C GLY* 2.9 34.0 + - - +
139C TYR* 3.7 31.4 - - + -
152C ALA* 4.5 15.0 - - - -
278C LEU* 3.9 31.6 - - + +
279C TYR* 4.0 9.3 - - + +
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Residues in contact with PHE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU* 6.2 0.2 - - + -
78C ASN* 3.8 8.5 - - - -
81C VAL* 3.6 35.9 - - + -
82C MET* 3.7 21.3 - - + -
85C LEU* 4.0 15.0 - - + -
94C LEU* 4.2 17.5 - - + -
95C VAL 2.8 20.3 + - - +
96C SER* 3.3 30.1 - - - -
97C GLU 3.0 23.2 + - - -
115C VAL* 4.1 15.9 - - + -
116C CYS* 1.3 75.8 - - - +
118C ASP* 1.3 59.8 + - - +
119C PRO* 3.9 16.2 - - + -
134C THR* 5.4 2.2 - - + -
135C ILE 3.1 14.4 - - - +
136C PHE* 4.1 9.4 - - + -
279C TYR* 3.6 11.2 - - - +
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Residues in contact with ASP 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C GLU* 3.6 27.8 - - - +
117C PHE* 1.3 73.5 - - - +
119C PRO* 1.3 70.1 - - - +
120C LEU 3.8 3.6 + - - +
121C ASP* 2.7 47.1 + - + +
134C THR* 3.4 3.1 - - - +
135C ILE* 2.9 31.0 + - + -
276C ARG* 4.2 1.7 + - - -
279C TYR* 3.9 21.4 - - + +
280C GLU* 3.4 12.8 - - - +
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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