Contacts of the helix formed by residues 240 - 248 (chain D) in PDB entry 4S10
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 PRO 240 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B ARG* 4.0 8.0 - - - +
100B LEU 3.5 14.8 - - - +
101B HIS 3.8 9.2 - - - +
102B ARG 4.5 2.9 - - - +
103B PRO* 3.8 21.8 - - + -
198D HIS* 3.4 31.6 - - + +
232D HIS* 5.0 0.2 - - + -
234D SER* 3.9 15.7 - - - -
238D THR 3.9 0.2 - - - -
239D GLU* 1.3 88.4 - - + +
241D GLU* 1.3 65.9 + - - +
242D ALA 4.0 0.4 - - - +
243D MET* 2.9 29.6 + - - +
244D LEU* 3.3 9.6 + - - +
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Residues in contact with GLU 241 (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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2B VAL* 4.3 0.8 - - + +
28B THR* 3.2 20.8 - - - +
29B PHE* 3.1 9.9 + - - +
30B SER* 3.0 40.8 + - - +
31B SER 4.1 6.0 + - - +
32B PHE* 3.8 26.0 - - + +
100B LEU* 3.5 31.1 + - + +
239D GLU 3.6 2.4 + - - -
240D PRO* 1.3 71.0 - - - +
242D ALA* 1.3 57.0 + - - +
244D LEU* 3.2 4.7 + - - -
245D GLN* 2.8 54.0 + - + +
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Residues in contact with ALA 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 2.9 26.5 + - + +
101B HIS* 3.4 41.5 - - + +
193D LEU* 4.4 4.6 - - + +
198D HIS* 4.0 5.6 - - + +
240D PRO 3.0 0.2 - - - -
241D GLU* 1.3 78.1 - - - +
243D MET* 1.3 62.5 + - - +
245D GLN* 3.4 15.5 + - - +
246D VAL* 3.5 19.6 + - - +
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Residues in contact with MET 243 (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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180D TRP* 3.8 13.7 - - + -
183D PHE* 4.1 7.6 - - + -
191D LEU* 3.9 19.7 - - + -
193D LEU* 5.2 0.2 - - - -
198D HIS* 3.9 34.1 - - + +
200D TRP* 3.4 41.5 - - + -
234D SER* 4.3 2.0 - - - -
239D GLU* 3.9 6.3 - - + -
240D PRO* 2.9 28.4 + - + +
242D ALA* 1.3 79.4 - - - +
244D LEU* 1.3 57.8 + - + +
246D VAL* 3.2 2.4 + - - +
247D LEU* 2.9 54.8 + - + +
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Residues in contact with LEU 244 (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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29B PHE* 3.3 36.6 - - + -
30B SER* 3.6 28.5 - - - +
180D TRP* 4.2 15.7 - - + -
239D GLU* 4.2 19.7 - - + +
240D PRO 3.8 10.3 - - - +
241D GLU* 3.2 7.5 + - - +
243D MET* 1.3 73.4 - - - +
245D GLN* 1.3 60.9 + - - +
248D GLY* 2.9 45.2 + - - +
249D PRO* 4.4 1.8 - - + -
250D LYS* 4.0 17.7 - - + +
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Residues in contact with GLN 245 (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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1B GLN 3.6 20.5 + - - +
2B VAL* 3.6 15.2 - - + +
27B ARG 3.1 27.7 + - - +
29B PHE* 4.0 11.9 - - - -
100B LEU* 5.2 5.6 - - + -
241D GLU* 2.8 41.6 + - + +
242D ALA* 3.6 13.0 - - - +
243D MET 3.3 0.2 - - - -
244D LEU* 1.3 73.4 - - - +
246D VAL* 1.3 64.4 + - + +
248D GLY* 4.5 1.6 + - - -
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Residues in contact with VAL 246 (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 GLN* 3.2 28.7 - - - +
178D VAL* 4.1 20.1 - - + +
191D LEU* 4.5 4.0 - - + -
193D LEU* 4.0 27.8 - - + -
242D ALA 3.6 12.6 - - - +
243D MET 3.2 7.0 + - - +
244D LEU 3.1 0.2 - - - -
245D GLN* 1.3 83.8 - - + +
247D LEU* 1.3 66.1 + - + +
248D GLY 3.4 0.4 - - - -
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Residues in contact with LEU 247 (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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162D LEU* 5.3 0.2 - - + -
178D VAL* 3.8 19.5 - - + +
179D SER* 3.6 39.5 - - - +
180D TRP* 3.3 35.2 + - + +
183D PHE* 4.0 17.9 - - + -
191D LEU* 3.9 17.5 - - + -
243D MET* 2.9 44.8 + - + +
246D VAL* 1.3 77.3 - - + +
248D GLY* 1.3 62.0 + - - +
249D PRO* 4.7 0.3 - - - +
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Residues in contact with GLY 248 (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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29B PHE* 4.4 6.7 - - - -
180D TRP* 3.0 13.2 + - - -
244D LEU* 2.9 30.8 + - - +
245D GLN 4.3 1.9 + - - -
246D VAL 3.4 2.8 + - - -
247D LEU* 1.3 83.5 - - - +
249D PRO* 1.3 71.2 - - - +
250D LYS 3.4 0.7 + - - -
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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