Contacts of the helix formed by residues 401 - 408 (chain E) in PDB entry 3SWD
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 ARG 401 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E LYS* 4.7 6.8 + - - +
399E TYR 3.3 5.3 + - - -
400E GLU* 1.3 101.4 + - + +
402E ILE* 1.3 64.3 + - - +
403E GLU* 3.2 7.2 + - - -
404E ASP* 3.0 40.5 + - - +
405E LYS* 3.5 23.4 + - - +
277J GLU* 2.8 33.4 - - - +
278J ASP* 3.3 26.3 + - - -
279J TRP* 5.5 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 402 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E PHE* 4.0 26.7 - - + -
234E GLU* 6.0 0.9 - - - +
237E THR* 5.1 6.1 - - + -
238E PHE* 4.3 18.6 - - + -
374E ALA* 4.4 19.3 - - + -
377E VAL* 5.2 6.3 - - + -
378E LEU* 5.1 3.8 - - + -
395E ILE* 4.1 14.4 - - + -
396E ASP* 6.0 0.9 - - - +
399E TYR* 4.1 38.3 + - + +
400E GLU 3.4 3.8 + - - -
401E ARG* 1.3 75.8 - - - +
403E GLU* 1.3 67.5 + - - +
405E LYS* 3.5 4.6 + - - +
406E LEU* 3.0 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 403 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E PHE* 3.6 24.1 - - + -
396E ASP* 5.4 0.7 - - - +
401E ARG* 3.8 1.2 - - - -
402E ILE* 1.3 87.6 + - - +
404E ASP* 1.3 64.5 + - - +
406E LEU* 4.7 0.2 - - - -
407E ARG* 2.9 46.8 + - - +
413E ILE* 3.8 27.8 - - + +
415E ARG* 2.8 47.5 + - + +
277J GLU* 3.0 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 404 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401E ARG* 3.0 31.0 + - - +
402E ILE 3.3 0.6 - - - -
403E GLU* 1.3 76.5 - - - +
405E LYS* 1.3 62.2 + - + +
407E ARG* 2.8 22.1 + - - +
408E ALA* 3.0 24.1 + - - +
276J GLY* 4.6 1.3 - - - -
277J GLU* 2.3 72.9 + - - +
278J ASP* 3.9 1.0 - - - +
279J TRP* 5.0 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 405 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E GLU 5.2 0.5 - - - +
16E VAL* 3.9 23.4 - - + +
17E THR 3.3 19.6 + - - +
19E SER* 2.9 27.5 + - - -
234E GLU* 3.0 25.6 + - - +
238E PHE* 3.7 22.2 - - + -
400E GLU* 3.7 23.5 + - - +
401E ARG* 3.5 17.6 + - - +
402E ILE* 4.1 2.7 - - - +
403E GLU 3.4 0.2 - - - -
404E ASP* 1.3 76.8 - - + +
406E LEU* 1.3 62.6 + - - +
408E ALA* 3.4 14.4 + - - +
409E LEU* 3.4 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LEU* 4.1 25.3 - - + +
238E PHE* 3.8 25.1 - - + -
241E ALA* 4.7 1.1 - - + -
377E VAL* 3.6 30.3 - - + -
378E LEU* 4.5 15.3 - - + -
381E CYS* 4.3 11.0 - - - -
402E ILE* 3.0 33.7 + - + +
403E GLU 4.0 2.2 - - - +
405E LYS* 1.3 73.4 - - - +
407E ARG* 1.3 61.6 + - - +
409E LEU* 2.8 24.3 + - + +
410E GLY 3.3 0.3 + - - -
411E ALA* 3.1 28.2 + - + +
413E ILE* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 407 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403E GLU* 2.9 27.0 + - - +
404E ASP* 2.8 33.1 + - - +
406E LEU* 1.3 75.7 - - - +
408E ALA* 1.3 58.6 + - - +
410E GLY* 3.0 19.6 + - - -
411E ALA* 3.8 20.7 - - - +
413E ILE* 2.8 40.9 + - + +
414E GLU* 4.4 7.5 - - - +
415E ARG 5.2 1.4 - - - +
275J VAL* 4.6 15.4 + - - +
276J GLY* 3.7 6.9 + - - -
277J GLU* 3.6 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 408 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E GLN 4.2 3.8 - - - +
14E GLY* 5.2 0.7 - - - -
15E GLU 4.7 12.0 + - - +
404E ASP 3.0 16.8 + - - +
405E LYS* 3.7 8.7 - - - +
406E LEU 3.2 0.4 - - - -
407E ARG* 1.3 76.0 - - - +
409E LEU* 1.3 62.0 + - - +
----------------------------------------------------------
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