Contacts of the helix formed by residues 246 - 258 (chain A) in PDB entry 1E5E
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 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 3.9 0.2 + - - -
84A SER* 5.1 1.4 - - - -
244A VAL 3.5 2.8 + - - -
245A ILE* 1.3 76.5 - - - +
247A PRO* 1.3 64.2 - - - +
248A HIS* 3.1 20.1 + - - +
249A ASP* 2.9 11.2 + - - +
250A ALA 2.8 25.1 + - - -
246B SER* 3.7 20.6 - - - -
249B ASP* 3.0 35.6 + - - -
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Residues in contact with PRO 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.1 2.9 - - - -
30A TYR 3.2 35.2 - - - +
31A GLN* 4.2 16.6 - - - +
32A THR 5.0 1.3 - - - +
57A THR* 4.0 14.8 - - + +
61A ASN* 3.6 24.5 - - - +
63A THR* 3.3 13.7 - - + +
64A VAL* 4.3 11.9 - - + -
245A ILE 3.5 5.6 - - - +
246A SER* 1.3 86.9 - - - +
248A HIS* 1.3 55.2 + - - +
250A ALA* 4.3 0.2 - - + -
251A TRP* 2.9 26.3 + - - +
216B ASP 5.7 0.2 - - - +
218B VAL 6.2 1.3 - - - +
249B ASP* 4.7 1.3 - - - +
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Residues in contact with HIS 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.8 23.1 - - + -
31A GLN* 3.1 20.9 + - - +
246A SER* 3.1 6.6 + - - +
247A PRO* 1.3 79.9 - - - +
249A ASP* 1.3 77.3 + - - +
251A TRP* 3.4 6.1 + + - +
252A LEU* 3.1 54.6 + - + +
31B GLN* 3.7 9.4 - - + -
248B HIS* 3.3 50.4 - + + +
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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
----------------------------------------------------------
217A VAL* 3.9 20.8 - - + +
218A VAL 4.2 9.5 + - - +
245A ILE* 4.3 9.3 - - + +
246A SER* 2.9 11.8 + - - +
248A HIS* 1.3 87.4 + - - +
250A ALA* 1.3 67.9 + - - +
252A LEU* 3.1 8.5 + - - +
253A ILE* 2.9 29.0 + - - +
31B GLN* 3.2 18.3 + - - -
246B SER* 2.8 41.7 + - - -
247B PRO* 4.8 1.0 - - - +
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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
----------------------------------------------------------
63A THR* 4.1 9.4 - - + +
64A VAL* 3.9 28.7 - - + -
67A LEU* 4.1 15.4 - - + +
245A ILE* 3.9 16.9 - - + +
246A SER 2.8 12.5 + - - +
247A PRO 3.7 6.5 - - - +
249A ASP* 1.3 76.7 - - - +
251A TRP* 1.3 57.7 + - - +
253A ILE* 3.2 4.0 + - - +
254A THR* 2.9 31.6 + - - -
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Residues in contact with TRP 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.8 23.6 - - + +
27A PRO* 3.2 25.5 + - + -
28A PRO* 4.4 2.2 - - - +
29A ILE* 3.5 46.6 - - + +
63A THR* 3.7 12.7 - - + +
247A PRO 2.9 17.2 + - - +
248A HIS* 3.5 6.7 - + - +
250A ALA* 1.3 78.9 - - - +
252A LEU* 1.3 82.7 + - + +
254A THR* 3.3 9.9 + - + -
255A ARG* 3.0 46.4 + - + +
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Residues in contact with LEU 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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212A ASN* 3.3 7.9 - - - +
216A ASP* 4.8 12.1 - - - +
217A VAL* 3.8 25.1 - - + -
248A HIS* 3.1 45.4 + - + +
249A ASP* 3.1 9.0 + - - +
251A TRP* 1.3 94.6 - - + +
253A ILE* 1.3 59.4 + - - +
255A ARG* 3.3 15.8 + - - +
256A GLY* 2.9 24.1 + - - -
31B GLN* 4.2 14.1 - - + +
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Residues in contact with ILE 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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67A LEU* 3.8 25.6 - - + -
207A ALA* 4.4 9.9 - - + -
211A ILE* 3.9 24.7 - - + +
212A ASN* 3.3 20.2 - - + +
217A VAL* 3.8 14.4 - - + -
219A ALA* 3.3 33.0 - - + -
221A LEU* 5.5 0.9 - - + -
245A ILE* 3.8 15.3 - - + -
249A ASP 2.9 19.4 + - - +
250A ALA 3.5 5.4 - - - +
252A LEU* 1.3 71.2 - - - +
254A THR* 1.3 56.8 + - - +
256A GLY* 3.1 2.1 + - - -
257A LEU* 2.7 33.5 + - - +
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Residues in contact with THR 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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12A CYS 5.0 1.2 - - - +
27A PRO* 6.4 1.1 - - + -
63A THR 5.0 1.2 + - - -
66A ASN* 4.0 15.4 + - - +
67A LEU* 3.5 29.2 + - - +
70A LYS* 4.0 27.6 - - + -
250A ALA 2.9 14.4 + - - -
251A TRP* 3.3 12.7 + - + -
253A ILE* 1.3 77.6 - - - +
255A ARG* 1.3 61.5 + - - +
257A LEU* 3.3 9.3 + - - +
258A SER* 3.3 19.8 + - - -
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Residues in contact with ARG 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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214A HIS* 6.0 3.8 + - - -
251A TRP* 3.0 41.1 + - + +
252A LEU* 3.4 19.1 - - - +
254A THR* 1.3 78.5 - - - +
256A GLY* 1.3 59.0 + - - +
258A SER* 2.6 27.2 + - - +
259A THR* 4.2 2.4 + - - +
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Residues in contact with GLY 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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211A ILE 3.6 1.6 - - - -
212A ASN 3.3 19.3 - - - -
214A HIS* 3.9 14.6 - - - -
252A LEU 2.9 13.7 + - - -
253A ILE 3.5 2.5 - - - -
255A ARG* 1.3 75.4 - - - +
257A LEU* 1.3 59.1 + - - +
259A THR* 3.1 14.1 + - - -
263A ARG* 2.8 26.3 + - - -
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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
----------------------------------------------------------
12A CYS* 3.3 25.3 - - + +
67A LEU* 4.5 7.4 - - + -
70A LYS* 4.0 32.8 - - + -
71A ILE* 4.0 16.2 - - + -
74A LEU* 3.7 19.5 - - + -
211A ILE* 3.5 21.9 + - + +
253A ILE* 2.7 21.2 + - + +
254A THR* 3.4 8.5 - - - +
256A GLY* 1.3 69.3 - - - +
258A SER* 1.3 65.3 + - - +
260A LEU* 3.0 42.2 + - + +
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Residues in contact with SER 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A CYS* 3.7 19.7 - - - -
13A ILE* 3.5 36.6 - - - +
254A THR 3.3 7.8 + - - -
255A ARG* 2.6 24.5 + - - +
256A GLY 3.2 0.2 - - - -
257A LEU* 1.3 79.3 - - - +
259A THR* 1.3 62.9 + - - +
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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