Contacts of the helix formed by residues 395 - 404 (chain H) in PDB entry 3E20
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 SER 395 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H TYR* 4.8 8.4 - - - -
280H GLU* 2.7 30.4 + - - +
281H LYS* 3.3 32.8 - - - +
394H ARG* 1.3 83.7 - - - +
396H GLN* 1.3 66.4 + - - +
397H GLU* 4.3 0.3 - - - +
398H GLY* 3.1 18.6 + - - -
399H MET* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 396 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577E TYR* 3.2 25.9 - - - -
578E SER* 3.1 38.5 - - - +
647E ASP* 3.2 22.1 + - - +
281H LYS* 5.0 3.8 - - - +
394H ARG 3.9 0.6 + - - -
395H SER* 1.3 70.5 - - - +
397H GLU* 1.3 79.6 + - - +
399H MET* 3.2 8.4 + - + +
400H GLN* 2.9 51.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 397 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H LYS* 3.2 58.6 - - + +
284H ILE* 3.8 22.2 - - + +
285H GLN* 3.6 33.2 - - - +
288H PHE* 4.0 15.3 - - + -
396H GLN* 1.3 86.3 + - - +
398H GLY* 1.3 64.6 + - - +
400H GLN* 2.9 10.3 + - - +
401H PHE* 2.8 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 398 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284H ILE* 3.7 15.1 - - - +
391H VAL* 5.6 1.1 - - - -
392H SER 3.5 22.0 - - - -
393H ASP* 4.1 6.1 - - - -
395H SER* 3.1 12.7 + - - -
397H GLU* 1.3 77.9 - - - +
399H MET* 1.3 62.8 + - - +
401H PHE* 2.9 3.7 + - - -
402H VAL* 2.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 399 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576E GLY* 3.7 19.3 - - - +
578E SER* 5.2 8.5 - - - -
393H ASP* 3.5 42.1 - - - +
395H SER 3.0 11.5 + - - +
396H GLN* 3.2 12.5 + - + +
398H GLY* 1.3 74.4 - - - +
400H GLN* 1.3 57.3 + - - +
402H VAL* 3.7 3.0 - - - +
403H LYS* 2.8 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 400 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572E ILE 3.9 12.4 + - - +
573E LEU* 4.1 0.6 - - - +
574E THR* 3.0 41.3 + - - +
576E GLY* 3.6 10.1 - - - +
577E TYR* 3.5 30.0 - - - +
288H PHE* 3.7 27.3 - - + -
396H GLN* 2.9 35.8 + - - +
397H GLU* 2.9 8.3 + - - +
399H MET* 1.3 71.5 - - - +
401H PHE* 1.3 58.5 + - - +
402H VAL 2.9 4.3 - - - -
404H GLY* 2.7 35.0 + - - -
405H PHE* 3.7 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 401 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284H ILE* 3.6 24.2 - - + -
287H PHE* 4.1 31.0 - + - -
288H PHE* 4.5 1.1 - - - -
318H LEU* 3.1 54.7 - - + -
319H CYS 4.2 0.2 - - - -
320H PHE 5.0 0.4 - - - -
391H VAL* 3.9 22.2 - - + -
397H GLU 2.8 10.0 + - - +
398H GLY 3.4 6.7 - - - +
400H GLN* 1.3 73.4 - - - +
402H VAL* 1.3 60.0 + - + +
405H PHE* 3.6 20.4 + + + +
407H GLY* 3.1 39.6 + - - -
408H ILE 3.7 4.5 - - - -
409H GLY* 3.5 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 402 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320H PHE* 3.6 52.9 - - + -
391H VAL* 6.1 0.9 - - + -
393H ASP* 3.8 16.6 - - + +
398H GLY* 2.8 19.9 + - - +
399H MET* 3.7 5.8 - - - +
400H GLN 2.9 1.2 + - - -
401H PHE* 1.3 80.3 - - + +
403H LYS* 1.3 61.8 + - + +
404H GLY 3.0 8.2 + - - -
406H GLY* 3.3 22.8 + - - -
407H GLY* 3.4 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 403 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575E THR* 3.4 20.8 - - + +
576E GLY* 4.1 14.1 - - - +
591E SER* 4.8 12.9 + - - +
592E PHE 5.7 2.9 - - - +
624E GLU* 5.2 7.5 + - - -
399H MET* 2.8 37.8 + - + +
402H VAL* 1.3 76.5 - - + +
404H GLY* 1.3 57.7 + - - +
406H GLY 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 404 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574E THR* 4.9 2.7 - - - -
575E THR* 4.2 17.5 - - - -
576E GLY 4.5 1.6 - - - -
611E MET* 5.1 4.7 - - - +
300H PHE* 4.6 4.3 - - - -
400H GLN* 2.7 16.7 + - - +
403H LYS* 1.3 81.7 - - - +
405H PHE* 1.3 77.8 + - - +
406H GLY 3.7 1.6 - - - -
----------------------------------------------------------
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