Contacts of the helix formed by residues 241 - 249 (chain D) in PDB entry 4DVQ
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 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D ARG* 6.0 4.0 - - - +
49D TRP* 6.2 0.9 - - + -
52D LEU* 4.9 2.7 - - + -
114D GLU* 4.3 6.7 - - - +
240D MET* 1.3 94.3 - - + +
242D ARG* 1.3 67.4 + - - +
243D SER* 3.6 17.3 - - - +
244D LEU* 3.1 33.5 + - + +
245D SER* 3.1 10.9 + - - -
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Residues in contact with ARG 242 (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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114D GLU* 3.9 19.1 + - + +
118D ALA* 4.3 11.5 + - + +
122D HIS* 6.1 0.6 - - - +
240D MET 3.7 1.4 + - - -
241D PRO* 1.3 71.1 - - - +
243D SER* 1.3 56.9 + - - +
244D LEU 2.9 1.9 + - - -
245D SER* 3.1 6.6 + - - -
246D ARG* 2.6 89.8 + - - +
253D TRP* 3.3 53.4 - - + +
257D PHE* 4.1 27.3 - - - -
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Residues in contact with SER 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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241D PRO* 3.6 16.1 - - - +
242D ARG* 1.3 77.3 - - - +
244D LEU* 1.3 61.6 + - - +
246D ARG* 4.4 13.8 - - - +
247D TRP* 3.4 20.1 + - - -
57E ARG* 5.2 1.2 + - - -
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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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49D TRP* 3.8 28.9 - - + -
52D LEU* 4.0 15.7 - - + -
240D MET* 3.4 14.1 - - + -
241D PRO* 3.1 32.8 + - + +
243D SER* 1.3 85.3 + - - +
245D SER* 1.3 55.2 + - - +
246D ARG 3.1 1.6 - - - -
247D TRP* 3.2 25.0 + - + +
248D ILE* 2.7 40.0 + - + +
50E LEU* 5.4 7.4 - - + -
53E LEU* 4.4 15.0 - - + -
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Residues in contact with SER 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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237D LEU* 3.9 14.5 + - - -
240D MET* 3.2 32.3 + - - +
241D PRO 3.1 3.7 + - - -
242D ARG* 3.1 9.4 + - - -
244D LEU* 1.3 76.8 - - - +
246D ARG* 1.3 63.7 + - - +
249D SER* 2.9 36.1 + - - +
250D PRO 3.5 0.2 - - - -
253D TRP* 2.6 38.7 + - - -
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Residues in contact with ARG 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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242D ARG* 2.6 77.6 + - - +
243D SER* 4.4 12.2 - - - +
245D SER* 1.3 74.6 + - - +
247D TRP* 1.3 59.5 + - + +
250D PRO* 3.8 16.9 - - - +
253D TRP* 4.3 9.0 - - - +
57E ARG* 6.3 0.7 - - - +
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Residues in contact with TRP 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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243D SER 3.4 25.2 + - - -
244D LEU* 3.2 23.7 + - + +
245D SER 3.1 0.2 - - - -
246D ARG* 1.3 80.1 - - + +
248D ILE* 1.3 86.7 + - + +
249D SER 3.2 1.1 - - - -
250D PRO* 3.3 14.3 - - - +
53E LEU* 3.3 33.0 - - + -
54E GLN* 5.5 0.2 - - - -
56E TRP* 4.1 18.8 - + - -
57E ARG* 3.5 71.4 - - + +
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Residues in contact with ILE 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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52D LEU* 3.8 17.7 - - + -
56D TRP* 3.6 37.7 + - + -
240D MET* 3.1 30.5 - - + -
244D LEU* 2.7 31.3 + - + +
247D TRP* 1.3 101.6 - - + +
249D SER* 1.3 68.7 + - - +
250D PRO* 3.5 2.3 - - - +
53E LEU* 4.6 5.8 - - + -
56E TRP* 4.0 20.4 - - + -
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Residues in contact with SER 249 (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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56D TRP* 4.0 10.7 - - - +
236D GLN* 5.1 5.7 + - - +
237D LEU* 4.8 2.9 - - - -
240D MET* 4.9 4.3 - - - -
245D SER* 2.9 23.5 + - - -
248D ILE* 1.3 92.5 + - - +
250D PRO* 1.3 60.3 - - - +
251D LYS* 3.1 3.4 - - - -
252D VAL* 2.8 41.5 + - - +
253D TRP* 3.2 11.3 + - - -
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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