Contacts of the strand formed by residues 248 - 253 (chain A) in PDB entry 4KM5
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 TYR 248 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLU* 4.0 3.3 - - - +
242A TYR* 3.1 25.7 + - + +
245A THR* 3.7 20.8 + - - +
246A ARG 3.7 0.6 - - - -
247A ALA* 1.3 99.0 - - + +
249A TYR* 1.3 66.1 + - - +
362A LYS* 3.7 26.2 - - + -
363A HIS* 2.7 36.7 + - - -
366A GLU 4.1 3.5 + - - -
370A PHE* 3.3 36.2 - + + -
374A THR* 4.0 13.0 - - - +
375A TRP 3.3 4.5 - - - +
376A ARG* 3.9 23.6 - - + -
488A PHE* 4.2 20.5 - + - -
495A LEU* 5.3 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 4.0 29.6 - - + -
240A GLU 3.5 4.5 - - - +
241A GLU* 3.6 38.6 - - + +
242A TYR 4.4 0.4 - - - +
246A ARG* 3.6 15.4 + - - -
247A ALA 4.3 0.2 - - - -
248A TYR* 1.3 83.7 - - - +
250A PHE* 1.3 67.6 + - - +
251A VAL* 5.3 0.2 - - - -
331A PRO* 3.6 17.2 - - + +
332A ALA 5.0 0.2 + - - -
333A SER* 2.8 30.8 + - - -
359A LEU* 4.8 4.0 - - + -
374A THR* 3.3 6.9 - - - -
375A TRP* 2.7 46.0 + - - +
377A LEU* 3.6 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLN 3.5 1.9 - - - +
239A LEU* 3.5 8.1 - - - +
240A GLU* 2.7 59.7 + - + +
241A GLU 5.2 0.9 - - - -
242A TYR* 3.4 29.4 - + + -
249A TYR* 1.3 73.1 - - - +
251A VAL* 1.3 60.1 + - - +
252A LYS* 4.9 1.1 - - - +
270A ILE* 3.7 33.0 - - + -
371A GLN* 3.4 41.1 - - + -
373A GLU* 3.5 31.9 - - + -
374A THR* 3.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A VAL* 6.0 0.9 - - + -
237A ILE* 3.7 20.9 - - + -
238A GLN 4.1 1.6 - - - -
239A LEU* 4.1 4.9 - - + -
249A TYR 4.0 0.6 + - - +
250A PHE* 1.3 75.6 - - - +
252A LYS* 1.3 65.0 + - - +
253A PHE* 4.9 5.2 - - + -
270A ILE* 3.4 3.7 - - - +
271A LEU* 2.7 64.5 + - + +
324A LEU* 4.1 7.4 - - + -
359A LEU* 3.8 27.8 - - + -
375A TRP* 3.4 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 3.7 7.8 - - - +
238A GLN* 2.7 57.9 + - + +
240A GLU* 2.7 40.8 + - + +
250A PHE 4.9 2.7 - - - +
251A VAL* 1.3 78.5 - - - +
253A PHE* 1.3 68.0 + - - +
269A GLU* 3.7 41.1 + - + +
270A ILE* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A VAL* 3.6 27.6 - - + -
235A PRO 4.7 2.0 - - - -
236A ARG* 4.0 13.0 - - + +
237A ILE* 5.2 0.9 - - + -
238A GLN* 4.5 5.0 - - - +
251A VAL* 4.9 4.9 - - + -
252A LYS* 1.3 87.2 - - - +
254A LYS* 1.3 62.9 + - - +
255A ARG 4.1 0.9 + - - -
256A ASN* 5.7 4.7 - - + +
257A PRO* 6.6 0.2 - - + -
260A ASN* 5.9 8.7 - - + -
262A LEU* 4.2 21.5 - - + -
263A SER* 5.7 1.1 - - - -
266A LEU* 3.5 33.0 - - + -
269A GLU 4.7 5.3 + - - -
271A LEU* 4.2 35.0 - - + -
----------------------------------------------------------
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