Contacts of the helix formed by residues 395 - 405 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ALA 3.1 18.3 + - - +
392C ALA* 4.0 7.6 - - - +
393C ALA 3.2 0.4 - - - -
394C ASP* 1.3 75.7 - - - +
396C LEU* 1.3 62.3 + - - +
397C LEU 3.5 1.1 + - - -
398C GLU* 3.7 8.7 + - - +
399C ARG* 3.4 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C ALA 3.6 10.0 + - - +
393C ALA* 3.3 20.5 + - + +
394C ASP 3.2 1.2 - - - -
395C ALA* 1.3 78.1 - - - +
397C LEU* 1.3 54.7 + - - +
399C ARG* 3.1 13.4 + - + +
400C VAL* 2.7 38.9 + - + +
415C ALA* 3.6 40.6 - - + +
416C ILE* 3.8 19.3 - - + +
419C VAL* 3.8 25.4 - - + -
457C VAL 6.1 0.2 - - - +
460C ILE* 4.4 6.5 - - + -
461C ALA* 5.3 4.7 - - + -
464C LEU* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 4.8 5.8 - - + -
393C ALA 4.7 0.8 + - - -
394C ASP 4.3 7.4 + - - +
395C ALA 3.5 0.4 - - - -
396C LEU* 1.3 76.6 - - - +
398C GLU* 1.3 58.3 + - + +
400C VAL* 3.8 0.5 - - - -
401C ARG* 2.9 61.0 + - - +
464C LEU* 3.8 30.1 - - + +
489C PHE* 3.9 43.5 - - + +
492C ILE* 4.1 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ASP 5.3 1.1 + - - +
395C ALA* 3.7 9.9 + - - +
396C LEU 3.3 0.4 - - - -
397C LEU* 1.3 79.3 - - + +
399C ARG* 1.3 62.5 + - + +
401C ARG* 3.5 19.5 + - - +
402C GLU* 3.2 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 399 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C ALA 5.2 2.6 + - - -
395C ALA* 3.4 26.7 + - + +
396C LEU* 3.1 18.2 + - - +
398C GLU* 1.3 75.6 - - + +
400C VAL* 1.3 60.0 + - + +
402C GLU* 3.3 16.2 + - - +
403C HIS* 3.0 47.1 + - + +
415C ALA* 3.8 36.0 + - + +
418C SER* 5.7 3.6 - - - -
419C VAL* 5.0 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 400 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 3.5 24.0 - - + -
396C LEU* 2.7 33.8 + - + +
397C LEU 3.9 3.4 - - - +
399C ARG* 1.3 68.5 - - - +
401C ARG* 1.3 59.8 + - - +
403C HIS* 3.2 7.8 + - - +
404C PHE* 2.9 45.3 + - + -
412C ALA* 4.0 15.7 - - + +
415C ALA* 4.9 3.1 - - + -
416C ILE* 4.1 29.2 - - + -
464C LEU* 4.4 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 3.6 18.2 - - + -
36C LYS* 5.9 1.8 - - - +
39C ASP* 2.8 42.7 + - - +
41C TYR* 5.8 2.9 - - - -
397C LEU* 2.9 47.2 + - - +
398C GLU* 3.7 29.5 - - - +
400C VAL* 1.3 76.3 - - - +
402C GLU* 1.3 62.2 + - + +
404C PHE* 3.4 2.8 + - - +
405C ASP* 3.1 36.7 + - - +
489C PHE* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C GLU* 3.2 17.4 + - - +
399C ARG* 3.3 17.7 + - - +
401C ARG* 1.3 80.2 - - + +
403C HIS* 1.3 64.8 + - + +
405C ASP* 3.4 16.4 + - - +
406C VAL* 3.4 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ARG* 3.0 41.3 + - + +
400C VAL* 3.2 6.2 + - - +
402C GLU* 1.3 79.5 - - + +
404C PHE* 1.3 55.9 + - - +
406C VAL* 3.3 12.6 + - - +
408C ALA* 2.6 46.1 + - - +
411C LEU* 3.6 53.9 + - + +
412C ALA* 3.9 13.5 - - + +
415C ALA* 4.8 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 404 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ALA* 3.4 27.8 - - + -
32C ILE* 4.1 24.4 - - + +
35C PHE* 3.7 39.0 - + + -
36C LYS* 5.4 2.8 - - - -
259C LEU* 5.9 0.3 - - - +
400C VAL* 2.9 39.6 + - + +
401C ARG 3.4 4.5 + - - +
403C HIS* 1.3 75.9 - - - +
405C ASP* 1.3 62.1 + - - +
406C VAL 3.3 0.2 - - - -
407C PRO* 3.5 16.2 - - - +
408C ALA 4.6 2.5 - - - +
409C MET* 3.7 31.4 - - + -
412C ALA* 3.7 22.9 - - + -
413C LEU* 6.6 0.2 - - + -
416C ILE* 6.3 0.2 - - + -
464C LEU 5.4 3.4 - - - -
467C PRO* 4.4 10.1 - - + -
468C VAL* 4.5 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 405 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 6.1 0.3 - - - -
36C LYS* 2.8 34.4 + - - -
259C LEU* 6.2 0.2 - - - +
288C ARG* 4.7 7.3 + - - -
401C ARG* 3.1 30.8 + - - +
402C GLU* 3.7 8.8 - - - +
403C HIS 3.2 0.6 - - - -
404C PHE* 1.3 76.7 - - - +
406C VAL* 1.3 65.1 + - - +
407C PRO* 3.6 1.0 - - - +
----------------------------------------------------------
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