Contacts of the helix formed by residues 268 - 278 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206D MET* 3.0 36.8 - - + +
207D LEU* 3.7 26.5 - - + -
210D ASP* 3.4 33.9 - - + +
211D VAL* 4.2 6.1 - - + -
264D VAL* 2.7 29.3 + - + +
267D LEU* 1.3 108.7 - - + +
269D SER* 1.3 65.0 + - - +
270D SER 3.2 2.7 - - - -
271D LYS* 3.1 18.4 + - + +
272D MET* 2.9 27.3 + - + +
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Residues in contact with SER 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A CYS* 4.0 22.9 - - - +
56A LYS* 3.8 18.5 - - - -
57A GLU* 2.5 37.5 + - - +
236D TYR* 4.8 1.2 + - - -
265D ILE* 3.0 21.5 + - - -
266D ASN 4.7 1.8 + - - -
267D LEU 3.8 1.2 - - - -
268D MET* 1.3 75.7 - - - +
270D SER* 1.3 63.9 + - - +
272D MET* 3.5 14.3 + - - +
273D LEU* 3.4 14.9 + - - +
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Residues in contact with SER 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 2.9 29.3 + - - -
267D LEU 5.3 1.7 + - - -
268D MET 3.2 1.0 - - - -
269D SER* 1.3 81.1 + - - +
271D LYS* 1.3 61.5 + - - +
273D LEU* 3.2 4.2 + - - +
274D GLN* 2.9 30.5 + - - +
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Residues in contact with LYS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D MET* 3.8 17.8 - - + +
210D ASP* 2.5 31.2 + - - +
267D LEU* 4.9 6.8 - - - +
268D MET* 3.1 32.5 + - + +
270D SER* 1.3 77.4 - - - +
272D MET* 1.3 64.9 + - - +
274D GLN* 4.2 12.1 - - - +
275D ILE* 3.1 28.1 + - - +
281D TYR* 3.9 21.2 - - + +
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Residues in contact with MET 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A CYS* 3.5 33.9 - - - -
203D PHE* 3.6 23.2 - - + -
206D MET* 4.6 2.2 - - + -
207D LEU* 3.9 17.3 - - + -
232D LEU* 4.4 23.3 - - + +
236D TYR* 3.3 39.7 - - + -
265D ILE* 5.0 5.4 - - - -
268D MET* 2.9 35.2 + - + +
269D SER* 3.6 6.3 - - - +
271D LYS* 1.3 76.7 - - - +
273D LEU* 1.3 58.7 + - - +
275D ILE* 3.4 5.9 - - - +
276D ASN* 2.9 26.5 + - - -
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Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A CYS 6.0 0.2 - - - +
54A LEU* 4.8 3.8 - - + +
57A GLU* 3.6 31.0 - - + +
58A LEU* 4.9 1.1 - - + -
120A ARG* 3.6 45.8 - - + +
121A ASN* 4.1 7.9 - - + +
122A VAL* 4.2 10.8 - - + -
150A ALA* 3.7 18.8 - - + -
236D TYR* 3.0 21.5 + - - +
269D SER 3.4 8.3 + - - +
270D SER 3.2 7.6 + - - +
272D MET* 1.3 80.1 - - - +
274D GLN* 1.3 60.0 + - - +
276D ASN* 3.1 7.1 + - + +
277D ALA* 2.9 26.3 + - + +
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Residues in contact with GLN 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D SER 2.9 17.3 + - - +
271D LYS* 3.4 9.2 + - - +
273D LEU* 1.3 72.6 - - - +
275D ILE* 1.3 52.9 + - - +
276D ASN 2.7 10.2 + - - -
277D ALA* 2.8 5.0 + - + +
278D ASP* 2.6 66.8 + - + +
281D TYR* 3.3 33.8 - - + +
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Residues in contact with ILE 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ILE* 3.6 13.1 - - + +
202D VAL* 4.4 5.8 - - + -
203D PHE* 3.8 28.5 - - + -
206D MET* 4.3 14.4 - - + -
271D LYS 3.1 12.2 + - - +
272D MET* 3.4 18.2 - - - +
274D GLN* 1.3 75.3 - - - +
276D ASN* 1.3 62.2 + - - +
278D ASP 4.4 4.5 - - - +
279D PRO* 5.5 0.2 - - - +
281D TYR* 3.4 15.4 - - + -
282D PHE* 3.7 40.4 - - + +
285D VAL* 3.8 37.9 - - + -
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Residues in contact with ASN 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ARG* 5.7 0.3 + - - -
150A ALA* 4.1 14.0 - - + +
151A PHE* 3.9 15.8 - - - +
152A GLY* 3.0 27.9 + - - -
153A ILE* 3.2 31.6 + - - +
203D PHE* 3.9 0.6 - - - -
236D TYR* 3.5 17.0 - - - -
237D MET* 3.4 20.3 - - - +
272D MET 2.9 23.2 + - - -
273D LEU* 3.1 9.6 + - + +
274D GLN 2.7 0.8 + - - -
275D ILE* 1.3 89.1 - - - +
277D ALA* 1.3 61.4 + - - +
278D ASP 3.4 0.9 + - - -
279D PRO* 4.9 4.9 - - - +
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Residues in contact with ALA 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG* 4.6 4.9 - - - +
121A ASN* 3.4 41.3 + - + +
273D LEU* 2.9 15.5 + - + +
274D GLN* 2.8 6.6 + - + +
276D ASN* 1.3 78.3 - - - +
278D ASP* 1.3 56.8 + - + +
279D PRO* 3.4 10.3 - - - +
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Residues in contact with ASP 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D GLN* 2.6 48.1 + - + +
275D ILE 4.4 3.4 - - - +
276D ASN 3.4 0.4 - - - -
277D ALA* 1.3 75.5 - - + +
279D PRO* 1.3 55.9 - - - +
280D HIS* 3.3 21.1 + - - +
281D TYR* 2.8 38.8 + - + +
282D PHE* 3.1 8.7 + - - +
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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