Contacts of the helix formed by residues 162 - 175 (chain D) in PDB entry 1EFU
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 GLU 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D VAL* 5.2 5.2 - - - +
161D ASP* 1.3 73.3 - - - +
163D GLU* 1.3 58.4 + - - +
165D VAL* 3.3 6.8 + - - +
166D LYS* 2.8 36.9 + - + +
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Residues in contact with GLU 163 (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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161D ASP* 3.2 14.9 + - - +
162D GLU* 1.3 79.2 - - - +
164D LEU* 1.3 62.7 + - - +
166D LYS* 3.3 16.5 + - - +
167D HIS* 3.0 56.5 + - + +
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Residues in contact with LEU 164 (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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160D ALA* 3.7 24.5 - - + -
161D ASP* 3.1 23.2 + - - +
163D GLU* 1.3 76.3 - - - +
165D VAL* 1.3 64.7 + - - +
167D HIS* 3.0 10.9 + - + +
168D ILE* 2.9 31.3 + - + +
244D LEU* 3.8 36.1 - - + +
245D LEU* 4.5 6.1 - - + -
248D HIS* 3.6 41.7 - - + +
250D ALA* 3.7 9.0 - - + -
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Residues in contact with VAL 165 (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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141D VAL* 3.9 16.2 - - + -
142D LEU 4.3 0.7 - - - -
143D GLY* 3.4 36.6 - - - +
155D VAL* 3.6 20.9 - - + +
157D ALA* 3.9 14.4 - - + -
160D ALA* 3.7 20.9 - - + -
161D ASP 3.1 15.2 + - - +
162D GLU* 3.8 5.8 - - - +
164D LEU* 1.3 75.3 - - - +
166D LYS* 1.3 57.4 + - - +
168D ILE* 3.5 8.3 + - + +
169D ALA* 3.0 26.5 + - - +
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Residues in contact with LYS 166 (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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348C GLU* 2.8 39.6 + - - +
143D GLY* 5.6 1.1 - - - -
144D SER 4.9 13.5 - - - +
145D TYR* 4.6 6.0 - - + +
162D GLU* 2.8 25.2 + - + +
163D GLU* 3.6 15.9 + - - +
164D LEU 3.1 0.2 - - - -
165D VAL* 1.3 76.2 - - - +
167D HIS* 1.3 87.9 + - - +
169D ALA* 3.2 7.8 + - - +
170D MET* 2.9 36.3 + - + +
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Residues in contact with HIS 167 (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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324C LYS* 4.5 5.8 + - - -
163D GLU* 3.0 39.9 + - + +
164D LEU* 3.0 14.4 + - + +
166D LYS* 1.3 106.7 + - - +
168D ILE* 1.3 58.8 + - - +
170D MET* 3.3 13.1 + - - +
171D HIS* 2.9 27.5 + - - +
233D PHE* 3.6 27.1 - - + -
234D VAL* 5.0 0.3 - - - +
235D MET* 3.7 32.1 - - + +
244D LEU* 6.2 0.8 - - - +
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Residues in contact with ILE 168 (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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155D VAL* 3.9 20.2 - - + -
157D ALA* 5.5 3.4 - - + -
164D LEU* 2.9 35.4 + - + +
165D VAL* 3.9 8.5 - - + +
167D HIS* 1.3 73.5 - - - +
169D ALA* 1.3 61.6 + - - +
171D HIS* 3.3 6.9 + - - +
172D VAL* 2.9 36.3 + - + +
228D LEU* 4.0 28.5 - - + -
233D PHE* 5.0 0.9 - - - -
241D VAL* 4.4 11.9 - - + -
244D LEU* 4.5 3.6 - - + -
245D LEU* 3.6 23.1 - - + -
252D VAL* 3.5 22.7 - - + -
255D PHE* 6.1 0.2 - - + -
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Residues in contact with ALA 169 (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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144D SER* 4.2 12.1 - - - +
145D TYR* 3.4 21.5 - - + +
153D VAL* 3.2 18.8 - - + +
155D VAL* 3.5 22.4 - - + +
165D VAL 3.0 17.9 + - - +
166D LYS* 3.2 7.2 + - - +
168D ILE* 1.3 74.7 - - - +
170D MET* 1.3 58.8 - - - +
172D VAL* 3.3 1.0 + - - +
173D ALA 3.0 23.2 + - - -
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Residues in contact with MET 170 (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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323C PHE* 3.4 37.2 - - + -
324C LYS* 5.0 0.2 - - - +
348C GLU* 4.0 28.9 - - + +
349C MET* 3.7 17.2 - - + +
145D TYR* 3.4 36.6 - - + -
166D LYS* 2.9 21.9 + - - +
167D HIS* 3.5 21.3 - - - +
169D ALA* 1.3 76.4 - - - +
171D HIS* 1.3 61.7 + - - +
173D ALA* 3.2 4.2 + - - +
174D ALA* 3.1 23.4 + - - +
234D VAL* 4.6 1.3 - - + -
235D MET* 3.8 18.6 - - + -
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Residues in contact with HIS 171 (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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167D HIS 2.9 16.7 + - - +
168D ILE* 3.6 7.6 - - - +
169D ALA 3.3 0.2 - - - -
170D MET* 1.3 77.6 - - - +
172D VAL* 1.3 55.7 - - - +
174D ALA 3.1 0.9 + - - -
175D SER* 2.7 46.8 + - - -
228D LEU* 3.3 31.0 - - + +
231D GLN* 2.6 37.1 + - + +
232D PRO 3.1 22.0 - - - -
233D PHE* 4.3 6.5 - - + -
234D VAL* 3.4 34.3 + - + +
241D VAL* 3.6 14.5 - - + +
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Residues in contact with VAL 172 (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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153D VAL* 3.6 20.4 - - + -
155D VAL* 4.5 4.7 - - + -
168D ILE* 2.9 28.1 + - + +
169D ALA 3.3 5.1 + - - +
171D HIS* 1.3 74.3 - - - +
173D ALA* 1.3 63.5 + - - +
176D LYS 2.9 20.4 + - - -
177D PRO* 3.9 16.4 - - + +
228D LEU* 4.2 20.2 - - + -
255D PHE* 3.9 34.1 - - + -
257D ARG* 3.4 19.9 - - + -
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Residues in contact with ALA 173 (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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349C MET* 4.3 3.6 - - + -
351C MET* 4.0 8.3 - - - +
145D TYR* 3.7 26.2 - - + -
151D ILE* 4.0 16.0 - - + +
153D VAL* 3.8 10.0 - - + +
169D ALA 3.0 13.9 + - - +
170D MET 3.4 9.9 - - - +
172D VAL* 1.3 76.3 - - - +
174D ALA* 1.3 58.9 + - - +
257D ARG* 3.0 33.9 + - - +
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Residues in contact with ALA 174 (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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321C PRO* 4.2 18.4 - - + -
349C MET* 4.3 5.8 - - - -
351C MET* 3.7 22.7 - - + +
170D MET 3.1 14.0 + - - +
171D HIS 3.1 4.4 + - - +
173D ALA* 1.3 80.1 - - - +
175D SER* 1.3 60.6 + - - +
176D LYS* 3.6 10.0 - - - +
234D VAL* 3.9 18.6 - - + -
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Residues in contact with SER 175 (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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171D HIS* 2.7 24.9 + - - -
174D ALA* 1.3 72.3 - - - +
176D LYS* 1.3 68.8 + - - +
177D PRO 3.4 1.1 - - - -
231D GLN* 3.0 35.3 + - - -
232D PRO 4.6 1.2 + - - -
234D VAL* 3.1 26.9 - - - +
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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