Contacts of the helix formed by residues 401 - 411 (chain C) in PDB entry 4X4S
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 GLY 401 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C GLN* 4.0 13.9 - - - -
299C ARG* 3.7 14.3 - - - +
398C HIS 4.3 7.8 + - - +
399C THR 3.2 7.7 + - - -
400C LEU* 1.3 75.6 - - - +
402C LYS* 1.3 66.3 + - - +
403C ASN 3.5 2.0 - - - -
405C GLY* 2.9 20.9 + - - -
2D G 3.3 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C GLN* 3.8 1.8 + - - -
398C HIS* 5.5 4.9 - - - +
401C GLY* 1.3 73.0 - - - +
403C ASN* 1.3 76.0 + - - +
405C GLY* 4.4 0.2 - - - -
406C GLU* 2.9 57.7 + - - +
1D G 3.8 43.1 - - - +
2D G 2.7 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C PRO* 3.9 13.8 - - + +
288C ILE* 3.9 34.3 - - + +
292C ASN* 5.4 0.9 - - - +
296C GLN* 2.9 28.4 + - - +
402C LYS* 1.3 92.9 - - - +
404C VAL* 1.3 67.2 + - - +
405C GLY 3.2 0.2 - - - -
406C GLU* 3.3 10.9 + - - +
407C SER* 3.2 20.8 + - - -
1D G 4.3 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 404 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C PHE* 3.5 26.2 - - + -
286C PRO* 4.1 9.9 - - + -
293C LEU* 4.1 14.8 - - + -
296C GLN* 2.9 31.4 + - + +
297C LEU* 3.9 20.6 - - + -
300C ALA* 4.1 10.8 - - + -
400C LEU 3.5 18.2 - - - +
403C ASN* 1.3 75.8 - - - +
405C GLY* 1.3 58.2 + - - +
407C SER* 3.2 3.7 + - - -
408C ILE* 3.0 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 405 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C TRP* 3.0 41.1 - - - +
398C HIS* 5.1 0.7 - - - -
400C LEU* 3.6 8.9 + - - -
401C GLY 2.9 18.1 + - - -
404C VAL* 1.3 78.6 - - - +
406C GLU* 1.3 55.5 + - - +
408C ILE* 3.5 4.0 + - - +
409C ARG* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C TRP* 4.2 16.3 - - + -
398C HIS* 6.1 0.7 - - + -
402C LYS* 2.9 47.0 + - - +
403C ASN* 3.3 14.1 + - - +
404C VAL 3.3 0.6 - - - -
405C GLY* 1.3 75.0 - - - +
407C SER* 1.3 61.7 + - - +
409C ARG* 3.5 20.1 + - - +
410C GLU* 3.2 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 407 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C PHE* 3.6 9.4 - - - -
284C ARG* 2.8 39.8 + - - +
286C PRO* 4.4 7.6 - - - -
403C ASN 3.2 11.8 + - - -
404C VAL 3.2 9.3 + - - -
406C GLU* 1.3 75.4 - - - +
408C ILE* 1.3 64.0 - - - +
410C GLU* 3.5 10.5 + - - +
411C TYR 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 408 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C VAL* 4.9 5.4 - - + -
283C PHE* 3.8 29.2 - - + -
304C ILE* 5.5 0.7 - - + -
329C LEU* 4.6 10.1 - - + -
393C ALA* 3.7 27.3 - - + +
397C TRP* 4.7 0.7 - - + -
400C LEU* 3.6 26.2 - - + -
404C VAL* 3.0 36.3 + - + +
405C GLY* 3.8 5.6 - - - +
407C SER* 1.3 74.8 - - - +
409C ARG* 1.3 65.5 + - - +
411C TYR* 3.4 11.9 + - - -
412C PHE* 3.3 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 409 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ALA 5.5 0.4 - - - -
397C TRP* 3.4 63.9 - - + +
405C GLY 3.1 14.9 + - - +
406C GLU* 3.6 23.4 + - - +
407C SER 3.2 0.4 - - - -
408C ILE* 1.3 78.9 - - - +
410C GLU* 1.3 77.6 + - - +
411C TYR* 3.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 410 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ARG* 6.1 0.7 - - - -
406C GLU* 3.2 24.7 + - - +
407C SER* 3.5 8.4 + - - +
408C ILE 3.4 0.2 - - - -
409C ARG* 1.3 92.2 + - - +
411C TYR* 1.3 65.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 411 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C LYS* 5.0 2.9 - - + -
283C PHE* 3.6 12.4 - - - +
284C ARG* 4.8 8.2 + - + +
326C PHE* 6.2 4.5 - + - -
407C SER 2.9 18.8 + - - +
408C ILE 3.5 5.2 - - - -
409C ARG 3.2 2.3 - - - -
410C GLU* 1.3 82.6 - - + +
412C PHE* 1.3 87.1 + - - +
413C GLU* 3.4 36.7 + - + +
----------------------------------------------------------
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