Contacts of the helix formed by residues 253 - 267 (chain A) in PDB entry 1F9O
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 VAL 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 3.7 38.1 - - + +
77A PHE* 4.1 10.3 - - + -
78A ASP* 3.8 23.3 - - - +
239A THR 5.1 0.2 - - - +
242A ALA* 4.0 10.1 - - + +
243A ASP* 3.9 34.6 + - - +
246A ALA* 4.4 2.5 - - + -
252A SER* 1.3 77.2 - - - +
254A SER* 1.3 64.1 + - - +
255A THR 3.1 2.9 - - - -
256A SER* 2.8 20.5 + - - -
257A VAL* 3.1 18.1 + - + +
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Residues in contact with SER 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ASP* 5.7 1.1 + - - -
252A SER* 3.3 17.2 + - - -
253A VAL* 1.3 76.5 - - - +
255A THR* 1.3 62.1 + - - +
257A VAL* 3.2 19.4 + - - +
258A GLY* 3.3 10.0 + - - -
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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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78A ASP* 5.7 4.9 - - - +
253A VAL 3.1 1.2 - - - -
254A SER* 1.3 76.7 + - - +
256A SER* 1.3 67.8 + - - +
258A GLY* 3.3 9.9 + - - +
259A LYS* 3.4 36.0 + - - +
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Residues in contact with SER 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.6 27.4 - - - -
78A ASP* 2.8 24.9 + - - -
81A TRP* 3.6 27.7 + - - +
239A THR* 3.9 2.7 - - - +
253A VAL* 2.8 13.8 + - - -
255A THR* 1.3 76.9 - - - +
257A VAL* 1.3 63.7 + - - +
259A LYS* 3.2 10.0 + - - +
260A ALA* 3.0 23.2 + - - +
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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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239A THR* 3.9 13.0 - - + -
243A ASP* 3.8 33.9 - - + +
253A VAL* 3.1 17.6 + - + +
254A SER* 3.4 11.9 - - - +
255A THR 3.2 0.2 - - - -
256A SER* 1.3 76.6 - - - +
258A GLY* 1.3 62.8 + - - +
260A ALA* 3.5 1.4 + - - +
261A THR* 3.0 22.5 + - - -
337A ASN* 3.5 28.5 - - + +
338A PHE* 3.9 22.4 - - + -
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Residues in contact with GLY 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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254A SER 3.3 10.2 + - - -
255A THR* 3.3 5.0 + - - -
256A SER 3.2 0.6 - - - -
257A VAL* 1.3 77.8 - - - +
259A LYS* 1.3 63.3 + - - +
261A THR* 3.4 6.1 + - - -
262A LYS* 3.1 24.0 + - - +
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Residues in contact with LYS 259 (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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81A TRP* 3.8 48.0 - - + -
82A SER* 5.3 4.5 - - - +
85A GLU* 3.4 30.0 + - - +
150A TYR* 3.3 30.7 - - + +
255A THR* 3.4 32.5 + - + +
256A SER* 3.2 9.0 + - - +
258A GLY* 1.3 76.8 - - - +
260A ALA* 1.3 57.2 + - - +
262A LYS* 3.2 6.2 + - - +
263A MET* 2.9 24.6 + - - +
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Residues in contact with ALA 260 (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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81A TRP* 3.7 20.3 - - + -
236A VAL* 3.7 20.0 - - - +
239A THR* 3.6 27.4 - - + -
256A SER 3.0 16.1 + - - +
257A VAL 3.8 3.8 - - - +
259A LYS* 1.3 76.9 - - - +
261A THR* 1.3 57.1 + - - +
263A MET* 3.3 4.3 + - - +
264A GLY* 3.0 22.2 + - - -
332A LEU* 4.7 0.5 - - - +
338A PHE* 4.4 8.7 - - + -
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Residues in contact with THR 261 (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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144A TYR* 5.0 1.1 - - - +
257A VAL 3.0 18.6 + - - -
258A GLY* 3.8 7.0 - - - +
259A LYS 3.2 0.2 - - - -
260A ALA* 1.3 72.9 - - - +
262A LYS* 1.3 68.2 + - - +
264A GLY* 3.3 2.1 + - - -
265A ASP* 3.1 19.8 + - - +
332A LEU* 4.4 8.0 - - - +
337A ASN 3.9 3.2 + - - +
338A PHE* 3.3 36.0 - - - +
339A LYS 3.7 6.7 - - - +
340A PRO* 3.5 31.8 - - + +
341A LYS* 4.6 4.9 - - + +
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Residues in contact with LYS 262 (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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85A GLU* 5.3 0.8 + - - -
144A TYR* 3.5 48.4 - - + +
150A TYR* 3.7 40.9 - - + +
258A GLY 3.1 14.7 + - - +
259A LYS* 3.7 8.7 - - - +
261A THR* 1.3 76.4 - - - +
263A MET* 1.3 62.6 + - - +
265A ASP* 3.0 12.6 + - - +
266A TYR* 3.2 36.7 + - + -
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Residues in contact with MET 263 (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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81A TRP* 3.9 28.9 - - + -
89A ILE* 4.1 12.6 - - + -
150A TYR* 3.5 16.5 - - + +
151A GLY* 4.5 1.8 - - - -
152A MET* 3.6 35.9 - - + +
232A ASP* 3.5 49.9 - - + +
235A ALA* 4.1 6.7 - - - -
236A VAL* 5.1 1.6 - - + -
259A LYS 2.9 13.7 + - - +
260A ALA* 3.5 10.5 - - - +
261A THR 3.2 0.2 - - - -
262A LYS* 1.3 78.0 - - - +
264A GLY* 1.3 57.8 + - - +
265A ASP 3.3 0.2 + - - -
266A TYR* 3.3 3.5 + - - +
267A LEU* 2.9 26.0 + - - +
300A TYR* 5.3 0.2 + - - -
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Residues in contact with GLY 264 (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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236A VAL* 4.4 6.2 - - - +
260A ALA 3.0 13.1 + - - -
261A THR 3.3 4.0 + - - -
262A LYS 3.3 0.2 - - - -
263A MET* 1.3 75.1 - - - +
265A ASP* 1.3 64.2 + - - +
267A LEU* 3.4 17.8 + - - +
268A ARG 3.7 1.0 + - - -
332A LEU* 3.8 23.3 - - - -
340A PRO* 5.3 0.9 - - - -
349A TRP* 2.9 25.0 + - - -
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Residues in contact with ASP 265 (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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140A LEU* 3.9 14.0 - - + +
144A TYR* 2.6 27.2 + - + +
261A THR 3.1 8.2 + - - +
262A LYS 3.0 11.6 + - - +
264A GLY* 1.3 79.7 - - - +
266A TYR* 1.3 61.2 + - - +
268A ARG* 3.1 45.5 + - - +
340A PRO* 3.5 17.1 - - + +
342A SER* 2.7 45.3 + - - -
345A GLY* 4.0 0.2 - - - -
349A TRP* 4.9 0.7 - - - +
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Residues in contact with TYR 266 (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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140A LEU* 4.1 31.5 + - + +
144A TYR* 3.5 35.4 - + - +
146A THR* 4.0 8.1 + - - +
148A MET 3.4 26.1 + - - -
149A LEU* 3.7 20.9 - - + -
150A TYR* 3.5 47.1 - - + +
262A LYS* 3.2 36.3 + - + +
263A MET 3.9 0.7 - - - +
265A ASP* 1.3 75.1 - - - +
267A LEU* 1.3 61.8 + - - +
268A ARG 3.0 6.8 + - - -
269A TYR* 3.2 24.9 + + - +
300A TYR* 3.7 17.4 + - + +
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Residues in contact with LEU 267 (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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227A ASN* 4.3 6.3 - - - +
229A PRO* 3.8 30.1 - - + +
232A ASP* 3.9 16.4 - - + +
233A ALA* 3.7 33.9 - - + +
236A VAL* 5.1 2.0 - - + -
263A MET 2.9 17.1 + - - +
264A GLY* 3.4 14.6 - - - +
265A ASP 3.2 0.6 - - - -
266A TYR* 1.3 75.9 - - - +
268A ARG* 1.3 56.9 + - - +
269A TYR 3.1 2.5 + - - -
270A SER* 2.8 36.2 + - - +
271A PHE* 4.6 0.3 - - - -
296A LEU* 4.1 3.8 - - + -
300A TYR* 4.0 9.5 + - + -
328A ALA* 6.1 0.2 - - + -
332A LEU* 5.6 0.2 - - + -
349A TRP* 3.8 28.0 - - + -
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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