Contacts of the strand formed by residues 257 - 261 (chain B) in PDB entry 3N6J
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 LEU 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ILE* 5.1 0.2 - - + -
221B VAL* 4.1 21.1 - - + -
233B ILE 4.1 1.8 - - - +
234B THR* 3.9 7.4 - - - +
235B LEU* 3.6 47.1 - - + +
250B CYS* 4.6 15.9 - - + -
253B LEU* 2.5 48.2 + - + +
254B ASN* 3.6 11.6 - - - +
256B VAL* 1.3 72.4 - - + +
258B THR* 1.3 65.6 + - - +
259B TYR* 3.8 13.4 - - - +
260B ALA* 4.9 8.5 - - + -
285B ILE* 4.3 14.3 - - + +
286B PRO* 5.0 1.9 - - - +
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LYS* 5.9 2.1 - - - -
232B ARG* 3.9 23.4 - - + +
233B ILE 3.1 28.3 + - - -
234B THR* 4.4 3.4 - - - -
254B ASN 5.1 2.2 - - - -
256B VAL 3.5 5.0 + - - -
257B LEU* 1.3 72.1 - - - +
259B TYR* 1.3 77.0 + - + +
286B PRO* 3.6 20.4 - - - +
310B ILE* 5.3 0.2 - - - +
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Residues in contact with TYR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 4.2 9.9 - - - +
206B LYS* 2.7 36.8 + - - -
234B THR* 3.3 45.0 - - + +
235B LEU 3.7 3.6 + - - -
257B LEU* 3.2 8.8 - - - +
258B THR* 1.3 94.5 - - + +
260B ALA* 1.3 63.1 + - - +
261B GLU* 4.8 1.3 - - + -
285B ILE* 4.4 4.7 - - - -
286B PRO* 3.2 24.9 - - + +
287B THR 4.2 0.4 - - - +
288B ALA* 3.6 28.9 - - + -
310B ILE* 3.7 25.1 - - + +
312B LEU* 5.4 2.0 - - + +
364B THR* 4.2 21.7 + - + +
365B ALA* 4.4 7.3 + - - +
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Residues in contact with ALA 260 (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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235B LEU* 4.0 5.8 - - + +
237B PRO* 5.9 1.8 - - + -
241B TRP* 6.3 0.7 - - + -
250B CYS* 5.1 3.8 - - - -
257B LEU* 4.9 11.0 - - + -
259B TYR* 1.3 75.3 - - - +
261B GLU* 1.3 60.7 + - - +
262B ASP 3.6 1.6 + - - -
263B PRO* 3.7 21.3 - - + +
279B PHE* 3.9 24.7 - - + -
285B ILE* 4.2 5.8 - - + +
286B PRO 3.0 6.8 + - - +
287B THR* 3.4 4.7 - - - -
288B ALA 3.0 20.9 + - - -
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Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LYS* 3.1 38.4 + - - +
235B LEU 2.9 19.5 + - - +
236B ASP* 3.1 37.6 - - + +
237B PRO* 3.3 8.9 - - - +
259B TYR* 4.1 2.1 + - + -
260B ALA* 1.3 70.3 - - - +
262B ASP* 1.3 82.9 + - - +
263B PRO 3.2 0.7 - - - -
288B ALA* 3.4 14.4 - - + +
290B ASN* 3.8 18.5 - - - +
312B LEU* 3.3 23.8 - - + +
340B HIS* 4.3 7.1 - - - -
367B ASP* 4.2 3.9 - - - +
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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
------------------------------------------------------------
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