Contacts of the helix formed by residues 245 - 250 (chain D) in PDB entry 5XVO
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 PHE 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D THR* 5.0 8.1 - - + -
7D VAL* 4.6 6.1 - - + -
41D LEU* 3.5 33.4 - - + -
43D GLU* 4.4 1.6 - - - -
178D TYR* 3.6 17.3 - + - -
182D LEU* 4.7 10.8 - - + -
241D LYS 3.7 16.6 + - - -
242D ARG* 3.2 44.3 + - - +
243D LYS 3.2 1.0 - - - -
244D LEU* 1.3 74.7 - - - +
246D ALA* 1.3 62.2 + - - +
247D LEU 3.0 6.8 + - - -
248D PHE* 3.0 40.1 + + - +
249D MET* 3.4 11.1 + - + +
103F ILE* 3.8 23.7 - - + +
105F PHE* 4.4 14.6 - + - -
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Residues in contact with ALA 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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228D ILE* 4.1 10.5 - - + -
242D ARG 4.3 0.6 + - - -
243D LYS 3.2 19.4 + - - +
244D LEU 3.0 0.4 - - - -
245D PHE* 1.3 77.9 - - - +
247D LEU* 1.3 55.1 + - - +
248D PHE 3.2 0.2 - - - -
249D MET* 3.6 23.9 - - + +
250D ASN* 2.7 53.4 + - - +
252D TYR* 4.3 1.3 - - - -
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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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179D GLY 4.8 2.7 - - - +
182D LEU* 4.4 17.3 - - + -
183D LEU* 4.8 10.3 - - + -
186D ILE* 6.4 0.4 - - + -
224D LEU* 3.9 28.3 - - + +
225D VAL* 4.6 12.8 - - + +
228D ILE* 4.2 14.4 - - + -
244D LEU* 3.1 34.3 + - + +
245D PHE 3.0 0.4 - - - -
246D ALA* 1.3 78.8 - - - +
248D PHE* 1.3 68.5 + - + +
250D ASN 4.1 2.1 - - - +
252D TYR* 3.6 24.2 - - - +
261D LEU* 3.4 41.4 + - + +
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Residues in contact with PHE 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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5D THR* 3.7 30.1 - - + +
38D ASP* 4.8 2.2 - - - +
39D VAL* 4.4 22.9 - - + -
63D LEU* 5.6 2.9 - - + -
182D LEU* 4.2 32.1 - - + -
186D ILE* 3.7 32.3 - - + -
245D PHE* 3.0 41.8 + + + +
247D LEU* 1.3 85.5 - - + +
249D MET* 1.3 56.1 + - - +
250D ASN 4.6 0.2 - - - -
260D PHE* 4.0 5.7 - - - +
261D LEU* 5.4 2.6 + - + +
262D THR* 4.4 16.6 - - + +
102F ARG* 2.4 34.3 + - - +
103F ILE* 4.0 6.3 - - + -
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Residues in contact with MET 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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242D ARG 5.7 1.8 - - - +
245D PHE* 3.4 4.8 + - + +
246D ALA* 3.1 31.5 + - + +
248D PHE* 1.3 79.0 - - - +
250D ASN* 1.3 70.6 + - - +
260D PHE* 3.4 15.8 - - - -
101F GLU* 6.1 0.9 - - - +
102F ARG* 4.2 18.5 - - + +
103F ILE* 3.3 33.4 - - + +
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Residues in contact with ASN 250 (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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228D ILE* 5.7 1.6 - - - +
246D ALA* 2.7 39.6 + - - +
247D LEU 4.1 4.0 - - - +
248D PHE 3.6 0.2 - - - -
249D MET* 1.3 86.7 - - - +
251D THR* 1.3 63.1 + - - +
252D TYR* 3.7 31.4 + - + +
260D PHE* 3.4 18.3 - - - -
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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