Contacts of the helix formed by residues 395 - 405 (chain B) in PDB entry 2X1L
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 ALA 395 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ALA 3.2 17.6 + - - +
392B ALA* 3.9 8.3 - - - +
393B ALA 3.2 0.6 - - - -
394B ASP* 1.3 75.8 - - - +
396B LEU* 1.3 64.6 + - - +
397B LEU 3.5 0.6 + - - -
398B GLU* 3.7 8.5 + - - +
399B ARG* 3.4 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ALA 3.6 8.5 + - - +
393B ALA* 3.2 23.1 + - + +
394B ASP 3.2 0.2 - - - -
395B ALA* 1.3 75.1 - - - +
397B LEU* 1.3 60.4 + - - +
399B ARG* 3.3 12.9 + - - +
400B VAL* 2.8 38.5 + - + +
415B ALA* 3.6 39.9 - - + +
416B ILE* 3.9 19.5 - - + +
419B VAL* 3.8 27.6 - - + -
457B VAL 6.1 0.2 - - - +
460B ILE* 4.5 5.4 - - + -
461B ALA* 5.4 4.9 - - + -
464B LEU* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 4.8 5.2 - - + -
393B ALA 4.6 0.8 + - - -
394B ASP 4.3 7.0 + - - +
395B ALA 3.5 1.2 - - - -
396B LEU* 1.3 76.7 - - - +
398B GLU* 1.3 60.9 + - + +
400B VAL* 4.1 0.2 - - - +
401B ARG* 3.0 61.3 + - - +
464B LEU* 3.8 28.8 - - + +
489B PHE* 3.8 42.0 - - + +
492B ILE* 4.1 19.9 - - + +
493B ALA 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ASP 5.3 2.0 + - - +
395B ALA* 3.7 8.1 + - - +
396B LEU 3.3 0.4 - - - -
397B LEU* 1.3 80.4 - - + +
399B ARG* 1.3 62.3 + - - +
401B ARG* 3.6 21.3 + - - +
402B GLU* 3.3 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ALA 5.4 1.3 + - - -
395B ALA* 3.4 25.1 + - - +
396B LEU* 3.4 22.1 - - + +
398B GLU* 1.3 76.3 - - - +
400B VAL* 1.3 70.5 + - + +
402B GLU* 3.4 15.6 + - - +
403B HIS* 3.0 37.5 + - + +
415B ALA* 3.4 36.3 + - + +
418B SER* 5.6 2.8 - - - -
419B VAL* 5.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 3.6 23.6 - - + -
396B LEU* 2.8 35.0 + - + +
397B LEU 4.1 2.2 - - - +
399B ARG* 1.3 72.6 - - + +
401B ARG* 1.3 59.3 + - - +
403B HIS* 3.2 7.5 + - - +
404B PHE* 3.0 42.8 + - + -
412B ALA* 3.9 25.6 - - + +
415B ALA* 4.7 2.0 - - + -
416B ILE* 4.0 20.2 - - + -
464B LEU* 4.4 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 3.6 18.0 - - + -
36B LYS* 5.9 2.0 - - - +
39B ASP* 2.8 43.8 + - - +
41B TYR* 6.0 1.1 - - - -
397B LEU* 3.0 47.0 + - - +
398B GLU* 3.7 30.2 + - - +
400B VAL* 1.3 77.4 - - - +
402B GLU* 1.3 61.3 + - + +
404B PHE* 3.3 3.1 + - - +
405B ASP* 3.2 35.1 + - - +
489B PHE* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B GLU* 3.3 20.8 + - - +
399B ARG* 3.5 15.1 - - - +
400B VAL 3.3 0.2 - - - -
401B ARG* 1.3 77.6 - - + +
403B HIS* 1.3 67.5 - - + +
405B ASP* 3.4 15.5 + - - +
406B VAL* 3.4 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ARG* 3.0 33.8 + - + +
400B VAL* 3.2 7.6 + - - +
402B GLU* 1.3 80.7 - - + +
404B PHE* 1.3 55.2 + - - +
406B VAL* 3.3 12.5 + - - +
408B ALA* 2.6 47.4 + - - +
411B LEU* 3.6 35.2 + - + +
412B ALA* 3.7 30.1 - - + -
415B ALA* 4.7 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 3.6 24.5 - - + -
32B ILE* 4.1 28.1 - - + +
35B PHE* 3.7 46.2 - + + -
36B LYS* 5.6 2.1 - - - -
259B LEU* 6.0 0.3 - - - +
400B VAL* 3.0 31.7 + - + +
401B ARG 3.3 5.6 + - - +
403B HIS* 1.3 77.2 - - - +
405B ASP* 1.3 60.8 + - - +
406B VAL 3.2 1.1 - - - -
407B PRO* 3.5 17.1 - - - +
408B ALA 4.5 2.7 - - - +
409B MET* 3.8 28.5 - - + -
412B ALA* 3.7 22.7 - - + -
413B LEU* 6.5 0.4 - - + -
416B ILE* 6.3 0.9 - - + -
464B LEU 5.5 3.8 - - - -
467B PRO* 4.6 4.5 - - + -
468B VAL* 4.5 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 6.1 0.5 - - - -
36B LYS* 2.8 35.5 + - - -
288B ARG* 4.5 7.8 + - - -
401B ARG* 3.2 28.8 + - - +
402B GLU* 3.8 9.5 - - - +
403B HIS 3.2 0.4 - - - -
404B PHE* 1.3 77.7 - - - +
406B VAL* 1.3 65.1 + - - +
407B PRO* 4.7 0.6 - - - +
----------------------------------------------------------
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