Contacts of the helix formed by residues 268 - 278 (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 MET 268 (chain E).
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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
----------------------------------------------------------
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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Residues in contact with SER 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 3.2 28.7 + - - -
267E LEU 5.2 2.4 + - - -
268E MET 3.2 1.0 - - - -
269E SER* 1.3 77.3 + - - +
271E LYS* 1.3 62.9 + - - +
273E LEU* 3.2 5.2 + - - +
274E GLN* 2.9 28.9 + - - +
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Residues in contact with LYS 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E MET* 3.7 17.9 - - + +
210E ASP* 2.4 41.2 + - - +
267E LEU* 5.0 6.9 + - - +
268E MET* 3.1 24.1 + - + +
270E SER* 1.3 77.9 - - - +
272E MET* 1.3 64.6 + - - +
274E GLN* 4.2 12.1 - - - +
275E ILE* 3.0 27.7 + - - +
281E TYR* 3.7 22.7 - - + +
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Residues in contact with MET 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B CYS* 3.8 30.5 - - - -
203E PHE* 3.7 27.5 - - + -
206E MET* 4.5 3.8 - - + -
207E LEU* 3.8 18.4 - - + -
232E LEU* 4.3 20.6 - - + +
236E TYR* 3.2 38.7 - - + -
264E VAL* 5.1 2.0 - - - +
265E ILE* 5.0 5.4 - - - -
268E MET* 2.8 38.4 + - + +
269E SER* 4.0 6.1 - - - +
270E SER 3.3 0.2 - - - -
271E LYS* 1.3 76.4 - - - +
273E LEU* 1.3 58.9 + - - +
275E ILE* 3.6 4.0 - - - +
276E ASN* 3.0 25.8 + - - -
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Residues in contact with LEU 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 4.7 3.4 - - + +
57B GLU* 3.8 27.4 - - + +
58B LEU* 5.3 1.1 - - + -
120B ARG* 3.6 45.8 - - + +
121B ASN* 4.0 3.4 - - + +
122B VAL* 4.0 15.9 - - + -
150B ALA* 3.5 19.5 - - + -
236E TYR* 3.3 18.8 - - - +
269E SER 3.6 9.0 + - - +
270E SER 3.2 8.1 + - - +
271E LYS 3.1 0.2 - - - -
272E MET* 1.3 79.9 - - - +
274E GLN* 1.3 60.6 + - - +
275E ILE 3.4 0.2 - - - -
276E ASN* 3.2 4.3 + - - +
277E ALA* 2.8 26.5 + - + +
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Residues in contact with GLN 274 (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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270E SER* 2.9 16.5 + - - +
271E LYS* 3.3 11.9 + - - +
273E LEU* 1.3 73.8 - - - +
275E ILE* 1.3 58.8 + - - +
276E ASN 2.7 5.8 + - - -
277E ALA* 2.8 4.9 + - - +
278E ASP* 2.6 59.8 + - + +
281E TYR* 3.3 33.1 - - + +
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Residues in contact with ILE 275 (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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153B ILE* 3.6 9.8 - - + +
202E VAL* 4.1 10.5 - - + -
203E PHE* 3.8 30.3 - - + -
206E MET* 4.3 8.3 - - + -
271E LYS 3.0 14.4 + - - +
272E MET* 3.6 16.2 - - - +
274E GLN* 1.3 76.1 - - - +
276E ASN* 1.3 72.4 - - - +
278E ASP 4.2 2.4 - - - +
281E TYR* 3.2 16.7 - - + -
282E PHE* 3.4 50.8 - - + +
285E VAL* 4.0 28.0 - - + -
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Residues in contact with ASN 276 (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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149B ARG* 5.5 0.3 + - - -
150B ALA* 4.0 22.1 - - + +
151B PHE* 4.2 7.2 - - - +
152B GLY* 3.0 31.3 + - - -
153B ILE* 3.4 18.1 + - - +
203E PHE* 3.9 0.2 - - - -
236E TYR* 3.5 6.7 - - - -
237E MET* 3.2 45.3 - - - +
272E MET 3.0 21.2 + - - +
273E LEU* 3.2 8.7 + - + +
274E GLN 2.7 1.8 + - - -
275E ILE* 1.3 86.8 - - - +
277E ALA* 1.3 60.1 + - - +
278E ASP 3.4 1.1 + - - -
279E PRO* 5.0 4.0 - - - +
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Residues in contact with ALA 277 (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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120B ARG 4.2 5.2 - - - +
121B ASN* 3.0 43.2 + - + +
273E LEU* 2.8 22.9 + - + +
274E GLN* 2.8 5.5 + - - +
276E ASN* 1.3 71.8 - - - +
278E ASP* 1.3 57.0 + - + +
279E PRO* 3.7 8.4 - - - +
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Residues in contact with ASP 278 (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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274E GLN* 2.6 47.3 + - + +
275E ILE 4.6 2.2 - - - -
276E ASN 3.4 1.0 - - - -
277E ALA* 1.3 75.2 - - + +
279E PRO* 1.4 56.3 - - - +
280E HIS* 3.0 24.4 + - - +
281E TYR* 2.7 36.8 + - - +
282E PHE* 2.9 9.7 + - - +
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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