Contacts of the helix formed by residues 242 - 257 (chain A) in PDB entry 3K3T
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A TYR* 3.4 26.9 - - - +
240A TYR* 3.4 3.5 - - - +
241A ASP* 1.3 91.1 + - - +
243A TYR* 1.3 64.7 + - - +
244A GLU* 3.4 13.3 + - - +
245A GLN* 3.1 15.2 + - - +
246A ALA* 3.1 17.0 + - - +
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Residues in contact with TYR 243 (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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156A PHE* 4.0 12.6 - + - -
159A ALA* 4.3 30.5 - - + +
160A THR* 4.4 9.0 - - + -
163A GLN* 4.2 11.7 - - + -
192A GLN* 2.5 42.3 + - - -
200A PRO* 6.1 0.9 - - - +
202A TYR* 3.4 47.9 - + - -
204A LEU* 4.0 21.5 - - + -
242A SER* 1.3 69.9 - - - +
244A GLU* 1.3 66.6 + - - +
246A ALA* 3.2 2.5 + - - +
247A PHE* 2.9 36.2 + - + -
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Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLN* 3.5 38.6 + - - +
166A LYS* 4.8 11.2 + - - +
242A SER* 3.4 12.0 + - - +
243A TYR* 1.3 78.8 - - - +
245A GLN* 1.3 62.9 + - - +
247A PHE* 3.4 2.4 + - - +
248A GLN* 3.1 47.6 + - + +
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Residues in contact with GLN 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A TRP* 6.4 0.2 - - - -
216A LYS* 5.7 1.6 - - - +
239A ALA 4.8 0.5 - - - +
240A TYR* 3.4 18.6 - - + -
241A ASP* 2.8 57.5 + - - +
242A SER* 3.1 10.6 + - - +
244A GLU* 1.3 72.8 - - - +
246A ALA* 1.3 67.4 + - - +
248A GLN* 3.2 19.1 + - + +
249A ASP* 3.0 22.9 + - + +
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Residues in contact with ALA 246 (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 TYR 3.1 27.1 - - - +
204A LEU* 3.8 14.8 - - + -
205A PHE* 5.2 1.8 - - + -
240A TYR* 3.5 30.0 + - + -
242A SER 3.1 10.9 + - - +
243A TYR 3.2 8.7 + - - +
245A GLN* 1.3 77.0 - - - +
247A PHE* 1.3 57.1 + - - +
249A ASP* 3.3 4.9 + - - +
250A TYR* 3.0 26.1 + - - +
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Residues in contact with PHE 247 (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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160A THR* 4.1 15.0 - - + -
163A GLN* 3.4 41.7 - - + +
164A ALA* 3.6 29.4 - - + -
167A ALA* 4.1 14.2 - - + +
178A LEU* 4.2 9.0 - - + -
182A ALA* 4.9 2.9 - - + -
204A LEU* 3.5 38.1 - - + -
205A PHE* 3.6 26.7 - + - -
243A TYR* 2.9 32.8 + - + +
244A GLU 3.9 2.5 - - - +
246A ALA* 1.3 69.8 - - - +
248A GLN* 1.3 60.0 + - - +
250A TYR* 3.6 6.3 - - + +
251A ALA* 2.9 30.8 + - - +
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Residues in contact with GLN 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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166A LYS* 6.0 4.9 - - - +
244A GLU* 3.1 41.1 + - + +
245A GLN* 3.2 24.6 + - + +
247A PHE* 1.3 76.6 - - - +
249A ASP* 1.3 61.9 + - - +
251A ALA* 3.4 6.5 + - - +
252A ASP* 3.0 22.7 + - - +
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Residues in contact with ASP 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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207A ILE* 5.1 1.4 - - - +
213A TRP* 3.6 10.5 - - + -
238A ARG* 2.7 33.7 + - - -
240A TYR* 2.6 44.8 + - + +
245A GLN* 3.0 8.2 + - + +
246A ALA 3.6 3.8 - - - +
248A GLN* 1.3 74.7 - - - +
250A TYR* 1.3 59.5 + - - +
252A ASP* 3.3 13.7 + - - +
253A LEU* 2.9 28.5 + - - +
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Residues in contact with TYR 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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167A ALA* 4.7 1.8 - - + -
171A LEU* 3.7 24.1 - - + +
178A LEU* 3.7 24.5 - - + +
181A GLN* 2.7 35.1 + - - -
205A PHE* 3.5 41.1 - + + -
207A ILE* 5.5 9.6 - - + -
240A TYR* 5.4 0.2 + - - -
246A ALA 3.0 14.1 + - - +
247A PHE* 3.6 12.8 - + - +
249A ASP* 1.3 76.3 - - - +
251A ALA* 1.3 61.9 + - - +
253A LEU* 3.2 7.2 + - + -
254A VAL* 2.8 51.7 + - + +
272A PHE* 3.8 16.3 - - - -
276A LEU* 4.0 7.1 - - - +
281A TYR* 5.6 2.2 - + - -
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Residues in contact with ALA 251 (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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167A ALA* 4.1 13.5 - - + +
170A SER* 4.1 20.1 + - - +
171A LEU* 4.5 6.1 - - - +
247A PHE 2.9 17.4 + - - +
248A GLN* 3.7 7.2 - - - +
249A ASP 3.3 0.2 - - - -
250A TYR* 1.3 80.2 - - - +
252A ASP* 1.3 57.6 + - - +
255A GLY* 2.8 30.6 + - - +
256A ASN* 4.7 0.5 - - - +
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Residues in contact with ASP 252 (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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248A GLN 3.0 12.8 + - - +
249A ASP* 3.5 18.3 - - - +
250A TYR 3.3 0.2 - - - -
251A ALA* 1.3 76.5 - - - +
253A LEU* 1.3 63.6 + - - +
256A ASN* 2.9 57.1 + - - +
257A SER 4.2 0.2 + - - -
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Residues in contact with LEU 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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207A ILE* 4.3 34.8 - - + -
238A ARG* 5.0 17.3 - - - +
249A ASP* 2.9 17.8 + - - +
250A TYR* 3.2 6.9 + - + +
252A ASP* 1.3 77.7 - - - +
254A VAL* 1.3 64.2 + - + +
257A SER* 3.1 45.2 + - - +
260A TYR* 3.9 27.0 - - + +
281A TYR* 6.3 0.7 - - + -
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Residues in contact with VAL 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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171A LEU* 4.1 12.7 - - + +
250A TYR* 2.8 53.3 + - + +
253A LEU* 1.3 82.8 - - + +
255A GLY* 1.3 61.9 + - - +
256A ASN 3.6 0.2 + - - -
257A SER 4.3 1.2 - - - +
260A TYR* 3.4 44.2 - - + +
261A ALA* 5.4 0.3 - - - -
263A VAL* 3.8 39.6 - - + +
276A LEU* 4.6 4.3 - - + -
281A TYR* 6.3 2.2 - - + -
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Residues in contact with GLY 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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171A LEU* 3.4 19.1 - - - +
251A ALA 2.8 19.9 + - - -
254A VAL* 1.3 78.4 - - - +
256A ASN* 1.3 67.3 + - - +
257A SER 5.2 0.4 - - - -
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Residues in contact with ASN 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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251A ALA 4.7 0.6 - - - +
252A ASP* 2.9 41.7 + - - +
255A GLY* 1.3 87.4 + - - +
257A SER* 1.3 64.4 + - - +
258A PRO* 3.4 9.9 - - - +
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Residues in contact with SER 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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2A SO4 2.7 22.5 + - - -
253A LEU* 3.1 30.4 + - - +
254A VAL 4.3 1.2 - - - +
256A ASN* 1.3 76.1 - - - +
258A PRO* 1.3 68.5 - - - +
259A ARG* 3.4 14.9 - - - +
260A TYR* 3.0 29.2 + - - +
261A ALA* 3.6 4.3 + - - -
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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