Contacts of the strand formed by residues 335 - 344 (chain B) in PDB entry 1KF9
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 ILE 335 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B PRO 4.2 7.2 - - - +
334B PRO* 1.3 78.4 - - - +
336B ALA* 1.3 68.6 + - + +
337B LEU* 3.2 4.6 + - - -
357B TRP* 3.5 5.4 - - - +
358B GLU* 2.8 56.7 + - + +
359B ALA 4.1 6.5 - - - +
360B PRO* 5.1 1.6 - - + -
361B ARG* 3.4 44.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ILE* 1.3 80.9 - - + +
337B LEU* 1.3 67.5 + - - +
338B ASN* 3.2 8.4 + - - +
356B ARG 3.6 6.1 - - - +
357B TRP* 3.7 3.5 - - - -
358B GLU* 4.0 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PRO* 4.2 3.4 - - + +
335B ILE 3.5 9.4 - - - +
336B ALA* 1.3 74.4 - - - +
338B ASN* 1.3 61.5 + - - +
355B VAL* 4.1 20.4 - - + -
356B ARG 3.6 2.7 - - - -
357B TRP* 3.2 23.8 - - + -
410B VAL* 4.1 11.0 - - + +
412B VAL* 3.4 28.3 - - + +
426B SER* 3.7 28.5 - - - +
427B GLU* 4.1 9.6 - - + +
429B LEU* 3.7 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ALA 3.2 6.3 + - - +
337B LEU* 1.3 75.1 - - - +
339B TRP* 1.3 83.8 + - - +
340B THR* 5.6 1.4 + - - -
354B GLN 4.0 0.5 - - - +
355B VAL* 4.8 0.2 - - - -
356B ARG* 2.9 38.0 + - + +
429B LEU* 3.8 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ASN* 1.3 96.2 + - - +
340B THR* 1.3 78.9 + - - +
341B LEU* 3.9 21.3 - - + -
353B ILE* 3.6 35.7 - - + -
354B GLN 3.4 9.9 - - - +
355B VAL* 4.3 2.7 - - + +
429B LEU* 3.6 21.9 - - + +
430B TYR 3.9 8.3 + - - -
431B VAL* 3.6 28.3 - - + +
432B THR* 3.1 31.2 - - - -
433B LEU* 3.6 24.5 - - + -
434B PRO* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ASN* 5.6 1.2 + - - -
339B TRP* 1.3 82.6 + - - +
341B LEU* 1.3 76.9 + - - +
342B LEU* 4.2 13.0 - - + -
353B ILE* 3.2 5.4 - - - +
354B GLN* 2.9 41.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B TRP* 3.9 18.9 - - + -
340B THR* 1.3 86.7 - - - +
342B LEU* 1.3 66.3 + - - +
343B ASN* 4.8 2.5 - - - +
344B VAL* 3.9 18.4 - - + -
351B ALA* 4.4 12.1 - - + -
352B ASP 3.4 18.6 - - - +
353B ILE* 3.9 13.5 - - + -
433B LEU* 4.3 7.6 - - + -
434B PRO* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B THR* 4.2 6.3 - - + -
341B LEU* 1.3 82.1 - - - +
343B ASN* 1.3 71.3 + - - +
352B ASP* 2.9 29.2 + - + +
353B ILE 3.9 12.3 - - - -
354B GLN* 3.8 35.4 - - + +
398B PRO* 4.1 20.6 - - + -
400B TYR* 5.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 5.1 2.0 - - - -
342B LEU* 1.3 92.5 - - - +
344B VAL* 1.3 67.7 + - - +
345B SER 4.4 0.2 + - - -
351B ALA* 3.5 3.5 - - - +
352B ASP* 3.0 36.2 + - - +
700C TYR* 3.5 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.9 24.9 - - + -
343B ASN* 1.3 83.1 - - - +
345B SER* 1.3 75.8 + - - +
346B LEU* 3.9 6.9 + - - +
348B GLY* 4.6 3.8 - - - -
350B HIS 3.6 13.5 - - - +
351B ALA* 4.5 8.7 - - + -
404B VAL* 5.2 2.7 - - + -
434B PRO* 5.0 5.4 - - + -
436B MET* 3.3 41.5 - - + -
700C TYR* 5.2 0.4 - - - +
701C SER* 4.3 2.9 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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