Contacts of the helix formed by residues 246 - 258 (chain A) in PDB entry 3SRF
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 LYS 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ILE* 3.6 8.9 - - - +
245A ARG* 1.3 91.5 - - + +
247A ALA* 1.3 65.3 + - - +
248A SER* 3.3 20.6 - - - +
249A ASP* 3.2 38.8 + - - +
250A VAL 4.0 0.5 + - - -
274A GLU* 4.4 10.8 + - - +
278A ARG* 3.7 26.2 - - - +
281A GLU* 3.5 13.7 - - - +
282A ILE* 3.8 9.2 - - - -
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Residues in contact with ALA 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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246A LYS* 1.3 66.6 - - - +
248A SER* 1.3 57.2 + - - +
249A ASP 3.0 10.6 + - - -
250A VAL* 3.1 19.7 + - - +
251A HIS* 3.1 26.1 + - + -
281A GLU* 2.9 50.4 + - + +
282A ILE* 3.9 7.0 - - - +
284A GLU* 4.8 1.8 - - - +
285A ALA* 4.4 6.3 - - + -
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS* 3.3 29.8 - - - +
247A ALA* 1.3 77.0 - - - +
249A ASP* 1.3 61.5 + - - +
251A HIS* 3.8 14.9 + - - +
252A GLU* 3.5 20.8 + - - +
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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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219A ALA* 3.3 31.8 - - + +
220A VAL* 4.6 1.0 - - - +
243A PHE 4.7 0.5 - - - +
244A ILE* 4.1 14.2 - - + -
245A ARG* 3.7 25.1 + - - +
246A LYS* 3.5 30.2 + - - +
247A ALA 3.0 0.6 - - - -
248A SER* 1.3 90.7 + - - +
250A VAL* 1.3 60.0 + - - +
251A HIS 3.2 0.9 - - - -
252A GLU* 3.1 7.3 + - - +
253A VAL* 3.0 33.8 + - - +
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Residues in contact with VAL 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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244A ILE* 3.8 20.2 - - + +
246A LYS 4.3 2.0 - - - +
247A ALA* 3.1 11.2 + - - +
249A ASP* 1.3 78.0 - - - +
251A HIS* 1.3 56.9 + - + +
253A VAL* 3.2 9.7 + - - +
254A ARG* 2.9 29.9 + - - +
266A ILE* 4.1 19.0 - - + +
268A SER* 3.5 20.6 - - - +
282A ILE* 4.2 6.3 - - + -
285A ALA* 3.7 33.7 - - + +
286A SER* 3.5 16.6 - - - +
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Residues in contact with HIS 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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247A ALA* 3.1 31.1 + - + +
248A SER* 3.8 11.3 - - - +
249A ASP 3.2 0.2 - - - -
250A VAL* 1.3 79.2 - - + +
252A GLU* 1.3 51.8 + - - +
254A ARG* 3.6 10.1 - - + +
255A LYS* 2.8 36.6 + - - +
284A GLU* 5.0 6.1 + - - -
285A ALA* 4.3 20.7 - - + +
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Residues in contact with GLU 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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219A ALA* 6.3 0.4 - - + -
220A VAL* 4.2 23.7 - - + +
248A SER 3.5 13.4 + - - +
249A ASP* 3.1 13.1 + - - +
251A HIS* 1.3 76.0 - - - +
253A VAL* 1.3 60.8 + - - +
255A LYS* 3.6 27.6 + - - +
256A VAL* 3.0 44.6 + - + +
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Residues in contact with VAL 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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220A VAL* 3.8 20.2 - - + -
228A LEU* 4.1 20.4 - - + +
239A VAL* 4.7 6.5 - - + -
241A ALA* 4.2 17.9 - - + -
244A ILE* 4.7 5.2 - - + -
249A ASP 3.0 21.6 + - - +
250A VAL* 3.4 10.3 - - - +
252A GLU* 1.3 73.1 - - - +
254A ARG* 1.3 57.9 + - - +
256A VAL* 3.3 7.2 + - - +
257A LEU* 3.0 35.1 + - + +
266A ILE* 3.8 28.5 - - + -
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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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250A VAL* 2.9 18.0 + - - +
251A HIS* 3.6 13.0 - - + +
253A VAL* 1.3 74.7 - - - +
255A LYS* 1.3 57.5 + - - +
257A LEU* 3.2 7.5 + - - +
258A GLY* 2.9 28.4 + - - +
261A GLY 5.8 0.7 - - - -
262A LYS* 4.6 19.0 + - - +
264A ILE 3.6 16.0 + - - -
266A ILE* 3.5 23.2 - - + +
285A ALA 3.3 24.2 + - - -
287A ASP* 2.8 42.8 + - - +
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Residues in contact with LYS 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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251A HIS 2.8 21.4 + - - +
252A GLU* 3.6 31.8 + - - +
254A ARG* 1.3 72.1 - - - +
256A VAL* 1.3 61.9 + - + +
258A GLY* 3.3 12.8 + - - +
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Residues in contact with VAL 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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220A VAL* 4.5 8.7 - - + -
225A ILE* 4.4 36.6 - - + +
228A LEU* 3.7 33.2 - - + -
229A LYS* 4.6 19.0 + - + +
252A GLU* 3.0 34.8 + - - +
253A VAL 3.6 4.5 - - - +
254A ARG 3.3 0.2 - - - -
255A LYS* 1.3 78.5 - - + +
257A LEU* 1.3 60.0 + - - +
258A GLY* 3.5 0.5 + - - -
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Residues in contact with LEU 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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228A LEU* 3.9 30.5 - - + +
231A GLY* 5.8 0.7 - - - -
232A VAL* 3.8 29.0 - - + +
239A VAL* 4.6 5.8 - - + -
253A VAL* 3.0 25.5 + - + +
254A ARG* 3.2 6.0 + - - +
256A VAL* 1.3 75.3 - - - +
258A GLY* 1.3 65.3 + - - +
260A LYS* 3.8 3.3 + - - +
261A GLY* 3.0 34.3 + - - +
264A ILE* 4.2 26.2 - - + +
266A ILE* 3.8 30.7 - - + -
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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 ARG* 2.9 15.5 + - - +
255A LYS* 3.3 12.1 + - - -
256A VAL 3.2 2.8 - - - -
257A LEU* 1.3 81.8 - - - +
259A GLU* 1.3 58.6 + - - -
262A LYS* 3.4 22.5 + - - +
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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