Contacts of the helix formed by residues 390 - 402 (chain A) in PDB entry 1T5A
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 TYR 390 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 4.1 6.5 - - - -
21A ALA* 4.5 5.2 - - - +
23A ALA 2.5 29.4 + - - -
24A ASP 3.2 18.7 + - - -
25A THR 3.5 6.7 - - - -
26A PHE* 4.1 24.5 - + + -
29A HIS* 3.4 42.0 - + + -
388A ALA 3.4 1.2 + - - -
389A ILE* 1.3 77.6 - - - +
391A HIS* 1.3 63.5 + - - +
392A LEU* 3.3 20.3 - - + +
393A GLN* 3.2 50.1 + - + +
394A LEU* 3.0 18.9 + - - +
400B ARG* 5.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 4.6 5.8 - - + +
386A GLU 3.7 17.4 + - - -
387A ALA 4.9 2.9 + - - -
389A ILE* 3.2 38.0 + - + +
390A TYR* 1.3 69.7 - - - +
392A LEU* 1.3 63.1 + - - +
394A LEU* 4.1 8.3 - - + +
395A PHE* 2.6 35.6 + - - +
421A PHE* 3.7 26.0 - + + -
445A ARG* 3.8 17.4 + - + -
446A PRO 4.6 1.1 - - - -
447A ARG* 3.7 58.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA 3.8 21.8 + - - +
22A MET* 5.1 2.2 - - - -
23A ALA 3.4 28.7 - - - +
24A ASP* 4.9 0.4 - - - -
390A TYR* 3.3 14.3 - - + +
391A HIS* 1.3 78.9 - - - +
393A GLN* 1.3 61.6 + - - +
395A PHE* 4.3 3.1 - - - +
396A GLU* 3.5 19.4 + - - +
396B GLU* 4.9 5.6 - - - +
400B ARG* 3.5 52.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.8 9.3 - - - +
390A TYR* 3.2 40.3 + - + -
392A LEU* 1.3 79.9 - - + +
394A LEU* 1.3 66.9 + - - +
396A GLU* 3.3 5.7 + - + +
397A GLU* 3.0 56.2 + - + +
400B ARG* 5.3 3.4 - - - +
26C PHE* 3.4 13.1 - - + +
393C GLN* 3.3 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASN* 5.1 11.2 - - - +
355A GLY* 6.4 2.2 - - - -
389A ILE* 4.0 25.1 - - + -
390A TYR 3.0 17.6 + - - +
391A HIS* 3.8 6.3 - - - +
393A GLN* 1.3 77.5 - - - +
395A PHE* 1.3 64.9 + - - +
397A GLU* 3.3 4.7 + - + +
398A LEU* 3.0 48.0 + - + +
445A ARG* 3.8 32.1 - - + +
27C LEU* 5.2 11.9 - - + -
30C MET* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A HIS 2.6 21.0 + - - +
392A LEU* 4.3 2.7 - - - +
394A LEU* 1.3 74.6 - - - +
396A GLU* 1.3 62.7 + - - +
398A LEU* 3.6 6.0 - - + +
399A ARG* 3.0 64.8 + - + +
414A VAL* 4.4 4.9 - - + -
417A VAL* 3.4 25.6 - - + -
418A GLU* 3.2 38.4 - - + -
421A PHE* 3.6 31.2 - + + -
444A TYR* 3.7 28.5 - + + +
445A ARG 5.8 0.7 - - - +
399B ARG* 4.4 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU 3.5 18.6 + - - +
393A GLN* 3.3 7.1 + - - +
394A LEU 3.2 0.4 - - - -
395A PHE* 1.3 81.2 - - - +
397A GLU* 1.3 64.5 + - + +
399A ARG* 2.7 34.4 + - - +
400A ARG* 2.9 55.6 + - - +
392B LEU* 5.1 3.6 - - - +
396B GLU* 3.0 41.2 - - + +
399B ARG* 4.8 0.4 - - - +
400B ARG* 4.8 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A GLN* 3.0 42.1 + - + +
394A LEU* 4.1 5.4 - - + +
396A GLU* 1.3 76.4 - - + +
398A LEU* 1.3 59.1 + - - +
400A ARG* 3.2 4.0 + - - +
401A LEU* 2.8 35.3 + - - +
24C ASP 5.1 0.2 - - - +
25C THR* 3.5 27.6 - - + +
26C PHE* 3.0 25.1 + - - +
27C LEU* 2.8 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASN* 3.9 25.6 - - + +
319A ARG* 5.3 1.3 - - - -
394A LEU* 3.0 48.6 + - + +
395A PHE* 3.6 4.7 - - - +
397A GLU* 1.3 74.5 - - - +
399A ARG* 1.3 58.4 + - - +
401A LEU* 3.8 1.8 - - - +
402A ALA* 2.9 31.6 + - - +
443A ARG* 3.7 25.4 - - - +
444A TYR* 3.9 31.3 - - + +
445A ARG* 4.0 7.4 - - + -
27C LEU* 4.0 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PHE* 3.0 59.0 + - + +
396A GLU* 2.7 27.4 + - - +
398A LEU* 1.3 74.3 - - - +
400A ARG* 1.3 66.6 + - + +
402A ALA* 3.3 20.3 + - - +
414A VAL* 3.9 8.1 - - + -
444A TYR* 4.5 8.3 - - + -
392B LEU* 6.2 1.6 - - - +
395B PHE* 4.3 10.3 - - - -
396B GLU* 4.5 1.6 - - - +
399B ARG* 2.3 35.2 - - - +
418B GLU* 2.8 44.0 + - - +
421B PHE* 6.1 1.0 - - - +
422B LYS* 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU* 2.9 38.9 + - - +
397A GLU* 3.7 7.0 - - - +
399A ARG* 1.3 78.7 - - + +
401A LEU* 1.3 63.0 + - + +
402A ALA 3.1 7.3 + - - +
24B ASP* 3.4 36.7 + - - -
390B TYR* 5.3 1.0 + - - -
392B LEU* 3.7 47.9 + - + +
393B GLN* 5.4 3.6 - - - +
396B GLU* 5.1 4.8 - - - +
25C THR* 5.0 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ARG* 3.9 31.4 - - + +
397A GLU 2.8 19.5 + - - +
398A LEU* 3.8 2.5 - - - +
400A ARG* 1.3 71.9 - - + +
402A ALA* 1.3 62.5 + - - +
403A PRO* 3.4 8.5 - - - +
25C THR* 4.1 14.1 - - + +
27C LEU* 3.6 41.1 - - + -
28C GLU* 3.5 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ARG 6.0 0.2 - - - -
398A LEU 2.9 19.3 + - - +
399A ARG* 3.3 16.3 - - - +
400A ARG 3.0 10.5 - - - +
401A LEU* 1.3 76.8 - - - +
403A PRO* 1.3 74.1 - - + +
404A ILE* 5.3 1.0 - - - +
443A ARG* 5.1 8.7 - - - +
444A TYR* 4.4 13.0 - - + +
422B LYS* 4.0 17.6 + - - +
----------------------------------------------------------
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