Contacts of the helix formed by residues 195 - 199 (chain B) in PDB entry 4EQU
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 THR 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ASP* 2.7 23.3 + - - +
159A LYS* 2.8 22.1 + - - +
194B GLY* 1.3 71.4 - - - -
196B PRO* 1.4 83.2 - - + +
197B TYR* 3.4 4.5 - - + -
198B TRP* 3.2 41.5 + - + +
199B MET* 3.6 7.8 + - - +
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Residues in contact with PRO 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A PRO* 3.9 35.7 - - + +
245A VAL* 4.0 4.7 - - + -
246A LEU* 3.7 23.1 - - + -
249A ILE* 3.0 26.0 - - - +
194B GLY 3.8 2.6 - - - +
195B THR* 1.4 96.4 - - + +
197B TYR* 1.3 70.0 + - + +
198B TRP 3.2 0.9 + - - -
199B MET* 3.2 21.0 + - + +
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Residues in contact with TYR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TRP* 5.3 0.5 + - - -
225A ILE* 3.7 17.0 - - - +
235A PRO* 3.7 25.3 - - + +
236A PRO* 4.1 11.1 - - - +
237A HIS* 3.6 22.4 - - - -
238A HIS* 4.0 15.0 + - - -
240A LEU 3.3 19.2 + - - -
242A PRO* 3.8 20.0 - - + +
245A VAL* 3.7 31.4 - - + -
249A ILE* 4.2 8.1 - - - +
195B THR* 3.3 3.5 + - + -
196B PRO* 1.3 88.6 - - + +
198B TRP* 1.3 81.4 + + + +
199B MET 3.8 0.3 + - - +
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Residues in contact with TRP 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ASP* 5.8 2.2 - - - +
158A LEU 3.3 24.9 - - - +
159A LYS* 3.4 21.2 - - + +
221A TRP* 3.6 4.5 - - - -
222A SER* 2.7 37.4 + - - -
225A ILE* 3.6 26.5 - - + +
226A THR* 3.6 14.8 + - - +
229A GLU* 2.9 44.9 + - - +
235A PRO* 3.8 23.8 - - + -
195B THR* 3.2 36.7 + - + +
196B PRO 3.2 0.6 - - - -
197B TYR* 1.3 99.2 - + + +
199B MET* 1.3 59.6 + - - +
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Residues in contact with MET 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ARG 6.1 0.2 - - - +
221A TRP* 3.3 10.8 + - - -
222A SER* 4.6 1.6 - - - -
246A LEU* 4.2 11.7 - - + -
249A ILE* 3.4 17.2 - - - +
192B PHE* 5.2 2.5 - - + -
193B ILE 4.2 11.7 - - - +
194B GLY* 3.1 37.0 - - - +
195B THR 3.7 11.0 - - - +
196B PRO* 3.2 21.5 + - + +
197B TYR 3.5 0.4 - - - -
198B TRP* 1.3 78.0 - - - +
200B ALA* 1.3 64.3 + - - +
203B VAL* 4.1 22.2 - - + +
204B VAL* 3.8 26.7 - - + -
207B GLU* 5.1 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