Contacts of the helix formed by residues 253 - 269 (chain E) in PDB entry 1H4L
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 CYS 253 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E GLU* 3.0 19.0 - - + +
252E SER* 1.3 77.2 - - - +
254E LYS* 1.3 65.4 + - - +
255E GLU* 3.1 18.2 - - - -
256E ALA* 2.8 34.2 + - + -
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Residues in contact with LYS 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU 4.7 6.0 + - - +
38B ASP* 4.7 18.0 - - - +
245E LEU* 5.5 6.4 - - - +
249E LEU* 3.4 35.0 - - + -
251E GLU 4.9 0.4 + - - +
252E SER 3.2 11.3 + - - +
253E CYS* 1.3 69.6 - - - +
255E GLU* 1.3 64.7 + - - +
257E PHE* 2.9 26.8 + - - +
258E TRP* 3.2 22.8 + - + +
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Residues in contact with GLU 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B HIS* 3.1 41.4 - - + +
253E CYS* 3.0 15.5 + - - -
254E LYS* 1.3 78.3 - - - +
256E ALA* 1.3 64.3 + - - +
258E TRP* 3.3 1.7 + - - -
259E ASP* 3.2 17.9 + - - +
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Residues in contact with ALA 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E GLU* 2.9 20.6 - - - +
253E CYS* 2.8 22.9 + - + +
255E GLU* 1.3 76.5 - - - +
257E PHE* 1.3 62.0 + - - +
259E ASP* 2.8 22.1 + - - +
260E ARG* 3.0 21.4 + - - +
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Residues in contact with PHE 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E ALA 5.0 1.3 - - - -
228E THR* 3.8 29.4 - - + -
231E TYR* 3.9 21.8 - + + -
245E LEU* 3.3 34.8 - - + -
248E PHE* 4.1 18.2 - - + -
249E LEU* 3.7 30.1 - - + -
251E GLU* 3.0 14.6 + - + +
254E LYS* 2.9 11.3 + - - +
256E ALA* 1.3 75.2 - - - +
258E TRP* 1.3 83.2 + + - +
259E ASP 3.0 0.9 + - - -
260E ARG* 3.1 25.1 + - - +
261E CYS* 3.3 29.3 + - - -
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Residues in contact with TRP 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.5 54.0 + - + +
45B PRO* 3.5 32.3 - - + -
49B LEU* 4.2 11.2 - - + -
71B HIS* 3.3 29.6 - - + +
74B LYS* 6.0 0.4 - - - -
76B LEU* 5.1 9.1 - - + +
231E TYR* 3.9 21.5 - + - -
245E LEU* 3.2 36.4 - - + +
249E LEU* 6.1 0.4 - - - +
254E LYS* 3.2 34.5 + - + +
255E GLU* 4.8 0.4 - - - -
257E PHE* 1.3 89.1 - + - +
259E ASP* 1.3 60.8 + - - +
261E CYS* 3.6 12.4 + - + +
262E LEU* 3.4 25.5 + - - +
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Residues in contact with ASP 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B HIS* 3.3 18.5 + - - +
255E GLU* 3.2 28.0 + - - +
256E ALA* 2.8 19.4 + - - +
258E TRP* 1.3 77.2 - - - +
260E ARG* 1.3 63.4 + - + +
262E LEU* 3.0 10.7 + - - +
263E SER* 2.9 27.7 + - - +
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Residues in contact with ARG 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E VAL* 5.9 0.2 - - - -
224E ALA* 3.8 13.5 + - - +
225E VAL* 3.7 33.6 - - - +
228E THR* 3.1 34.5 + - + -
251E GLU* 2.4 40.3 + - - +
256E ALA* 3.0 16.9 + - - +
257E PHE* 3.1 16.8 + - - +
259E ASP* 1.3 76.2 - - - +
261E CYS* 1.3 53.6 + - - +
263E SER* 4.1 7.6 - - - -
264E VAL* 2.7 43.5 + - + +
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Residues in contact with CYS 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 4.1 23.8 - - + -
228E THR* 3.8 16.8 - - - -
231E TYR* 4.1 14.1 - - - -
232E LEU* 4.0 9.3 - - + +
257E PHE* 3.3 42.2 + - - -
258E TRP* 3.6 15.0 - - + +
259E ASP 3.1 0.4 - - - -
260E ARG* 1.3 78.4 - - - +
262E LEU* 1.3 59.2 + - + +
265E ILE* 3.0 37.0 + - - +
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Residues in contact with LEU 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 4.7 9.6 - - + -
52B ILE* 4.5 13.5 - - + -
69B VAL* 3.8 33.0 - - + +
70B LEU 4.9 0.7 - - - -
71B HIS* 3.7 33.7 - - + +
76B LEU* 4.2 11.7 - - + -
258E TRP 3.4 12.7 + - - +
259E ASP* 3.0 11.4 + - - +
261E CYS* 1.3 73.6 - - + +
263E SER* 1.3 61.6 + - - +
265E ILE* 3.2 5.7 + - + +
266E ASN* 2.8 50.0 + - - +
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Residues in contact with SER 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E ASP* 2.9 19.3 + - - +
260E ARG* 3.5 12.9 - - - +
262E LEU* 1.3 78.2 - - - +
264E VAL* 1.3 65.5 + - - +
266E ASN* 3.2 7.4 + - - +
267E LEU* 3.1 21.6 + - - +
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Residues in contact with VAL 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E LEU* 4.2 15.3 - - + -
211E VAL* 3.7 43.3 - - + -
228E THR* 4.8 7.4 - - + -
229E CYS* 5.0 4.3 - - - -
232E LEU* 3.7 23.8 - - + -
260E ARG* 2.7 31.5 + - + +
263E SER* 1.3 73.4 - - - +
265E ILE* 1.3 53.0 + - - +
267E LEU* 3.1 4.8 + - - -
268E MET* 2.7 45.5 + - + +
272E MET* 5.5 0.4 - - - -
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Residues in contact with ILE 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 3.5 49.6 - - + +
52B ILE* 3.9 24.2 - - + -
53B CYS* 3.7 26.5 - - - -
56B LYS* 4.1 9.6 - - + -
232E LEU* 4.0 17.0 - - + -
261E CYS 3.0 27.4 + - - +
262E LEU* 3.7 7.2 - - + +
264E VAL* 1.3 76.7 - - - +
266E ASN* 1.3 61.3 + - - +
269E SER* 2.9 38.3 + - - +
272E MET* 5.0 3.1 - - - -
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Residues in contact with ASN 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 5.5 1.9 - - - +
56B LYS* 2.6 43.8 + - - +
69B VAL* 5.8 4.3 - - - +
262E LEU* 2.8 42.1 + - - +
263E SER* 3.7 6.3 - - - +
265E ILE* 1.3 74.9 - - - +
267E LEU* 1.3 57.8 + - - +
269E SER* 4.7 1.6 - - - -
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Residues in contact with LEU 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E ASP* 3.7 23.3 - - + +
211E VAL* 4.6 4.9 - - + -
263E SER 3.1 14.2 + - - +
264E VAL* 3.1 4.4 + - - +
265E ILE 3.1 0.4 - - - -
266E ASN* 1.3 81.3 - - - +
268E MET* 1.3 95.0 + - + +
269E SER 3.7 0.4 - - - -
270E SER* 5.2 2.5 + - - -
271E LYS* 5.0 7.9 + - - +
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Residues in contact with MET 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206E MET* 3.0 35.9 - - + +
207E LEU* 3.7 28.5 - - + +
210E ASP* 3.1 36.6 - - + +
211E VAL* 4.3 3.6 - - + -
264E VAL* 2.7 29.9 + - + +
267E LEU* 1.3 106.7 - - + +
269E SER* 1.3 63.6 + - - +
270E SER 3.1 3.9 + - - -
271E LYS* 3.1 14.8 + - + +
272E MET* 2.8 30.2 + - + +
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Residues in contact with SER 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B CYS* 4.0 20.8 - - - +
56B LYS* 3.5 20.5 + - - +
57B GLU* 2.4 43.5 + - - +
236E TYR* 5.0 1.0 + - - -
265E ILE* 2.9 21.1 + - - -
266E ASN* 4.7 1.7 - - - -
267E LEU 3.7 1.4 - - - -
268E MET* 1.3 76.9 - - - +
270E SER* 1.3 62.6 + - - +
272E MET* 3.7 11.8 + - - +
273E LEU* 3.6 12.5 + - - +
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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