Contacts of the helix formed by residues 247 - 258 (chain A) 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 SER 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A ASP* 4.3 7.0 + - - -
122A GLY* 4.7 9.0 - - - -
125A ASN* 4.3 9.2 - - - +
130A VAL* 4.3 7.0 - - - -
131A SER 2.8 32.3 + - - -
132A VAL* 4.0 7.4 + - - -
245A VAL* 4.6 0.7 - - - -
246A GLY* 1.3 76.9 - - - +
248A MET* 1.3 65.8 + - - +
249A VAL 4.2 2.3 + - - -
250A ALA* 3.1 24.9 + - - +
251A ASP* 3.2 13.5 + - - +
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Residues in contact with MET 248 (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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121A ASP* 3.4 20.4 + - - +
135A ILE* 4.5 2.9 - - - -
246A GLY 4.1 1.0 - - - -
247A SER* 1.3 68.8 - - - +
249A VAL* 1.3 58.6 + - + +
251A ASP* 3.1 7.8 + - - +
252A VAL* 2.8 40.1 + - + +
262A PHE* 4.5 13.7 - - + -
275A LEU* 3.9 36.1 - - + -
280A GLU* 4.0 28.0 - - - +
284A MET* 3.5 42.8 - - + -
316A ILE* 4.4 12.3 - - + -
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Residues in contact with VAL 249 (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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121A ASP* 3.5 11.1 + - + +
133A GLY* 4.2 17.3 - - - +
135A ILE* 3.6 31.4 - - + -
164A TYR* 3.5 30.8 - - + -
165A ALA 3.8 5.4 - - - +
166A LEU* 3.5 25.6 - - + -
247A SER* 3.3 2.8 - - - +
248A MET* 1.3 74.8 - - - +
250A ALA* 1.3 62.0 + - - +
252A VAL* 4.4 0.3 - - - +
253A HIS* 3.0 23.0 + - - +
284A MET* 3.7 13.9 - - + -
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Residues in contact with ALA 250 (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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131A SER* 3.9 26.7 - - - +
166A LEU* 3.8 14.2 - - + +
245A VAL* 4.0 25.1 - - + -
247A SER* 3.1 13.3 + - - +
249A VAL* 1.3 77.4 - - - +
251A ASP* 1.3 59.6 + - - +
253A HIS* 3.6 1.6 - - - +
254A ARG* 3.0 30.0 + - - +
128B CYS 5.0 2.6 - - - +
130B VAL* 5.2 8.0 - - + +
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Residues in contact with ASP 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A SER* 4.6 2.5 - - - +
244A TYR* 3.9 12.4 - - - -
245A VAL* 3.1 21.8 + - - +
246A GLY* 3.1 23.7 + - - -
247A SER 3.4 10.4 + - - +
248A MET 3.1 8.2 + - - +
250A ALA* 1.3 75.6 - - - +
252A VAL* 1.3 63.1 + - - +
254A ARG* 2.8 29.2 + - - +
255A THR* 2.9 27.6 + - - -
262A PHE* 3.8 27.0 - - + +
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 4.5 10.3 - - + +
248A MET* 2.8 49.4 + - + +
249A VAL 4.4 0.4 - - - +
251A ASP* 1.3 71.6 - - - +
253A HIS* 1.3 63.3 + - - +
255A THR* 3.1 7.5 + - - -
256A LEU* 2.9 20.7 + - + +
262A PHE* 4.4 5.6 - - + -
284A MET* 4.0 29.6 - - + +
287A VAL* 5.1 3.1 - - + -
288A MET* 3.7 23.3 - - + -
318A LEU* 3.9 20.0 - - + -
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Residues in contact with HIS 253 (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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164A TYR* 2.6 31.7 + + + +
166A LEU* 3.5 22.2 - - + +
172A MET* 3.9 31.1 - - + -
174A VAL* 4.1 10.1 - - + -
183A CYS* 5.0 3.1 - - - -
249A VAL 3.0 20.1 + - - +
250A ALA 3.6 1.8 - - - +
252A VAL* 1.3 76.1 - - - +
254A ARG* 1.3 64.2 + - - +
256A LEU* 2.9 16.7 + - + +
257A VAL* 2.9 38.9 + - + +
127B ASP 4.5 2.0 + - - -
128B CYS 3.4 27.6 - - - -
129B LEU* 4.1 8.7 - - + +
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Residues in contact with ARG 254 (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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208A ILE* 3.8 30.3 - - - +
210A SER* 3.0 25.6 + - - -
243A ARG* 3.6 31.6 + - - +
245A VAL* 4.2 10.1 - - - +
250A ALA 3.0 12.6 + - - +
251A ASP* 2.8 32.4 + - - +
253A HIS* 1.3 76.8 - - - +
255A THR* 1.3 74.8 + - - +
258A TYR* 2.8 40.4 + - + +
259A GLY 4.7 1.1 - - - +
261A ILE 5.4 0.6 + - - -
128B CYS* 3.7 36.3 + - + +
130B VAL* 5.2 8.3 - - + +
245B VAL 5.8 0.4 + - - -
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Residues in contact with THR 255 (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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202A ILE* 3.1 9.1 - - + +
251A ASP 2.9 15.3 + - - -
252A VAL* 3.1 12.5 + - - -
254A ARG* 1.3 89.8 + - - +
256A LEU* 1.3 56.9 + - - +
259A GLY* 2.8 33.2 + - - +
260A GLY* 3.9 14.0 - - - +
261A ILE 4.6 4.5 + - - -
262A PHE* 4.1 11.0 - - - +
288A MET* 3.9 11.2 - - + -
318A LEU* 4.4 8.3 - - + +
319A GLY* 3.8 28.7 - - - -
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Residues in contact with LEU 256 (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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164A TYR* 3.6 20.4 - - - +
174A VAL* 4.2 19.7 - - + -
181A VAL* 4.6 6.1 - - + -
183A CYS* 4.8 8.1 - - - -
200A VAL* 4.6 14.6 - - + +
201A LYS 4.6 2.6 - - - +
202A ILE* 3.7 28.1 - - + +
203A LYS 4.8 0.9 + - - -
252A VAL* 2.9 12.2 + - + +
253A HIS* 2.9 13.0 + - + +
255A THR* 1.3 78.0 - - - +
257A VAL* 1.3 65.5 - - + +
259A GLY 4.2 0.2 + - - -
287A VAL* 4.2 12.6 - - + -
288A MET* 4.1 16.6 - - + +
291A ALA* 3.6 31.2 - - + -
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Residues in contact with VAL 257 (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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203A LYS* 5.5 3.5 + - - +
253A HIS* 2.9 48.8 + - + +
254A ARG 4.0 1.8 - - - +
256A LEU* 1.3 84.3 - - + +
258A TYR* 1.3 59.9 + - - +
127B ASP* 3.8 26.2 - - + +
128B CYS* 4.2 13.7 - - - -
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Residues in contact with TYR 258 (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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203A LYS* 3.3 38.3 + - - +
206A GLY* 4.5 0.7 - - - -
207A LYS* 4.4 27.4 - - + +
208A ILE* 3.7 34.0 - - + +
254A ARG* 2.8 20.9 + - + +
257A VAL* 1.3 79.1 - - + +
259A GLY* 1.3 66.5 + - - +
128B CYS* 4.4 17.0 - - - -
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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