Contacts of the strand formed by residues 242 - 247 (chain D) in PDB entry 3F7F
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 HIS 242 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ASP* 4.4 8.5 - - - +
236D VAL 3.4 2.6 - - - +
237D LEU* 3.6 2.2 - - - -
238D THR* 2.9 38.8 + - - +
240D ASN* 3.7 33.1 + - + +
241D CYS* 1.3 74.6 - - - +
243D LEU* 1.3 59.7 + - - +
244D LYS* 3.4 12.8 + - - -
256D ASP* 3.3 22.0 + - - +
257D TYR 3.2 17.8 + - - +
258D ASP* 3.8 28.5 + - + -
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Residues in contact with LEU 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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235D ILE* 3.4 28.7 - - + -
236D VAL 3.2 18.4 - - - +
237D LEU* 4.8 2.9 - - + -
241D CYS 3.9 1.6 + - - -
242D HIS* 1.3 71.0 - - - +
244D LYS* 1.3 57.7 + - - +
245D ILE* 3.5 7.1 + - + +
256D ASP* 3.9 0.2 - - - -
257D TYR* 2.8 40.4 + - + -
259D MET* 3.6 26.0 - - + +
280D LEU* 4.2 16.4 - - + -
287D LEU* 4.4 8.7 - - + -
289D THR* 5.3 0.2 - - - +
303D LEU* 5.6 1.1 - - + -
313D TYR* 3.6 44.9 - - + -
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Residues in contact with LYS 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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203D SER* 4.0 24.0 + - - +
206D LYS* 4.8 8.1 - - - +
221D ASP* 3.6 26.7 + - - +
234D LEU 3.9 0.9 - - - +
236D VAL* 2.8 48.7 + - + +
238D THR* 4.2 14.3 - - + +
242D HIS* 3.4 11.5 + - + +
243D LEU* 1.3 71.7 - - - +
245D ILE* 1.3 60.0 + - - +
246D TRP* 4.0 10.6 + - + +
253D LEU* 3.6 22.2 - - + -
255D GLN 3.4 5.4 - - - -
256D ASP* 3.7 33.2 - - - +
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Residues in contact with ILE 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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233D TYR* 4.2 5.8 - - + -
234D LEU 4.1 3.1 - - - +
235D ILE* 4.5 22.2 - - + -
243D LEU* 3.5 10.0 + - + +
244D LYS* 1.3 74.8 - - - +
246D TRP* 1.3 70.2 + - - +
253D LEU* 3.7 1.7 - - - +
254D ILE* 2.8 29.3 + - + +
255D GLN* 3.2 27.5 + - + -
257D TYR* 3.8 23.1 - - + +
303D LEU* 4.6 9.6 - - + -
311D LEU* 3.2 37.9 - - + -
313D TYR* 4.4 13.5 - - + +
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Residues in contact with TRP 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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183D LEU* 3.1 39.9 - - + +
199D PHE* 4.3 15.3 - + + -
200D ASN* 3.4 30.1 - - - -
201D ASP* 4.6 13.5 - - + -
203D SER* 6.0 1.1 - - - -
233D TYR* 3.1 6.6 - - - +
234D LEU* 2.7 57.3 + - + +
236D VAL* 4.2 16.9 - - + +
244D LYS* 4.0 16.2 - - + +
245D ILE* 1.3 76.9 - - - +
247D ASP* 1.3 62.0 + - - +
248D LEU* 3.8 6.4 + - + -
251D PHE 4.1 5.4 - - - -
252D THR* 3.4 10.8 - - - -
253D LEU* 3.0 58.9 - - + +
254D ILE* 4.5 0.2 - - - -
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Residues in contact with ASP 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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232D ARG* 3.4 13.9 + - - -
233D TYR* 3.2 32.3 - - + -
246D TRP* 1.3 72.0 - - - +
248D LEU* 1.3 53.6 + - - +
249D THR* 2.9 28.3 + - - -
250D SER* 3.7 13.1 + - - +
251D PHE* 2.5 37.0 + - - -
252D THR 3.4 7.2 + - - -
254D ILE* 3.2 30.6 - - + +
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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