Contacts of the helix formed by residues 362 - 377 (chain B) in PDB entry 3HN3
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 ASP 362 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ARG* 3.6 21.8 + - - +
360B GLY 3.7 1.9 + - - +
361B PHE* 1.3 85.7 - - - +
363B TRP* 1.3 63.6 + - - +
364B PRO* 3.3 8.9 - - - +
365B LEU* 2.9 35.2 + - + +
366B LEU* 3.0 22.7 + - - +
357E ARG* 2.9 40.6 + - - -
362E ASP* 3.5 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 5.6 1.3 - - - -
361B PHE* 3.5 21.4 - + - -
362B ASP* 1.3 68.3 + - - +
364B PRO* 1.3 76.9 - - + +
366B LEU* 3.2 35.9 + - + +
367B VAL* 3.0 26.5 + - - +
391B GLU* 3.8 27.1 - - + -
395B MET* 5.3 0.9 - - + -
42E ASP* 4.8 3.9 + - + -
43E GLY* 3.5 33.3 - - - +
44E LEU* 3.5 40.4 - - + -
78E PRO* 3.9 14.4 - - + -
79E VAL 5.1 3.8 - - - +
80E PRO* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ASP* 3.3 18.6 - - - +
363B TRP* 1.3 92.7 - - + +
365B LEU* 1.3 56.9 + - - +
367B VAL* 3.4 1.7 + - - +
368B LYS* 2.9 30.0 + - - +
78E PRO* 3.8 12.8 - - + -
80E PRO 3.9 20.6 - - - +
81E SER* 4.2 6.1 - - - +
86E ILE* 4.0 14.1 - - + +
356E ILE* 4.3 6.1 - - + -
357E ARG* 3.3 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ALA* 3.3 31.2 - - + -
357B ARG* 3.9 17.0 - - - +
362B ASP* 2.9 29.7 + - + +
364B PRO* 1.3 71.7 - - - +
366B LEU* 1.3 60.1 + - - +
368B LYS* 3.7 2.2 - - + +
369B ASP* 2.9 38.5 + - - +
611B ARG 5.3 1.6 - - - +
612B GLN* 5.9 0.7 - - - -
613B ARG* 4.0 35.2 - - + +
356E ILE* 4.1 23.1 - - + -
357E ARG* 4.2 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B PHE* 3.9 14.1 - - + -
362B ASP 3.0 15.8 + - - +
363B TRP* 3.3 43.3 - - + +
365B LEU* 1.3 77.2 - - - +
367B VAL* 1.3 64.4 + - + +
369B ASP* 3.3 4.5 + - + +
370B PHE* 3.1 53.0 + - + -
391B GLU 4.4 4.0 - - - +
392B VAL* 3.8 28.7 - - + -
395B MET* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B TRP 3.0 14.9 + - - +
364B PRO 4.0 2.5 - - - +
366B LEU* 1.3 73.5 - - + +
368B LYS* 1.3 67.1 + - - +
370B PHE* 3.1 3.1 + - - +
371B ASN* 2.9 31.6 + - - +
395B MET* 4.3 13.5 - - + -
399B TYR* 4.7 5.6 - - - +
44E LEU* 3.6 31.4 - - + -
76E ASP* 3.9 22.7 - - + +
78E PRO* 4.0 13.2 - - + -
86E ILE* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ASP 4.2 7.1 + - - -
553A PRO* 5.4 0.2 - - - +
364B PRO 2.9 18.5 + - - +
365B LEU* 3.7 5.6 - - - +
367B VAL* 1.3 76.5 - - - +
369B ASP* 1.3 57.6 + - - +
371B ASN* 3.2 3.3 + - - +
372B LEU* 2.9 41.3 + - + +
613B ARG* 4.1 20.8 + - + -
614B GLN* 4.8 5.4 - - - +
85E ASP 3.0 24.9 + - - +
86E ILE* 3.2 22.8 + - - +
87E SER 3.6 6.5 + - - -
88E GLN* 2.7 31.8 + - - +
356E ILE* 3.8 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LYS* 3.0 24.1 + - - +
365B LEU 2.9 22.2 + - - +
366B LEU* 3.6 7.0 - - + +
368B LYS* 1.3 76.5 - - - +
370B PHE* 1.3 62.2 + - + +
372B LEU* 3.2 4.1 + - - +
373B LEU* 2.9 32.5 + - - +
589B PHE* 3.4 20.1 - - + -
613B ARG* 2.8 50.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LYS* 6.0 2.0 - - - -
366B LEU* 3.1 37.5 + - + -
367B VAL 3.1 7.5 + - - +
369B ASP* 1.3 77.6 - - + +
371B ASN* 1.3 66.2 + - - +
373B LEU* 3.3 13.3 + - + +
374B ARG* 3.0 29.0 + - - +
381B PHE* 4.0 12.6 - + - -
392B VAL* 3.7 9.9 - - + -
395B MET* 3.6 39.3 - - + -
396B CYS* 3.7 41.1 - - - -
399B TYR* 3.9 28.5 - + + -
401B ILE* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B VAL* 2.9 23.4 + - - +
368B LYS 3.6 7.2 - - - +
370B PHE* 1.3 75.5 - - - +
372B LEU* 1.3 56.8 + - - +
374B ARG* 3.5 5.9 + - - +
375B TRP* 2.9 29.2 + - - +
399B TYR* 4.6 12.5 + - - -
75E VAL* 6.1 0.5 - - - +
76E ASP 5.4 1.2 + - - -
86E ILE* 2.9 41.6 + - - +
87E SER* 3.8 13.1 - - - +
88E GLN* 4.0 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ASP* 5.9 0.4 - - + -
368B LYS* 2.9 22.3 + - + +
369B ASP 3.5 6.5 - - - +
371B ASN* 1.3 74.6 - - - +
373B LEU* 1.3 60.1 + - - +
375B TRP* 3.5 10.6 - - + +
376B LEU* 2.8 32.3 + - - +
589B PHE* 3.9 20.9 - - + -
609B PHE* 3.6 29.8 - - + -
613B ARG* 3.7 45.8 - - + +
615B PRO* 5.8 2.7 - - + -
88E GLN* 3.6 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B VAL* 3.6 31.4 - - + -
350B LYS* 4.4 9.4 - - + -
369B ASP 2.9 20.7 + - - +
370B PHE* 3.6 26.0 - - + +
372B LEU* 1.3 75.2 - - - +
374B ARG* 1.3 62.1 + - - +
376B LEU* 3.3 3.1 + - + +
377B GLY 3.2 3.3 + - - -
378B ALA* 3.0 46.2 + - + -
380B ALA 5.0 0.9 - - - +
381B PHE* 3.9 31.2 - - + -
401B ILE* 4.5 14.8 - - + -
589B PHE* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 2.7 66.8 + - + +
297B PRO* 5.0 10.0 - - - +
370B PHE 3.0 18.3 + - - +
371B ASN* 3.9 6.7 - - - +
373B LEU* 1.3 76.7 - - - +
375B TRP* 1.3 63.2 + - - +
377B GLY 3.2 8.1 + - - -
399B TYR* 3.6 42.1 + - + +
401B ILE* 4.7 7.9 - - + -
627B TRP* 3.4 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ASP* 3.3 23.7 + - + -
371B ASN 2.9 19.0 + - - +
372B LEU* 3.5 11.9 - - + +
374B ARG* 1.3 77.2 - - - +
376B LEU* 1.3 79.9 + - + +
609B PHE* 3.7 28.0 - + - -
615B PRO* 4.3 14.4 - - + -
619B ALA* 4.5 8.1 - - + -
620B PHE* 3.6 33.9 - + - -
623B ARG* 3.0 64.6 + - - +
627B TRP* 3.0 16.0 + - - -
88E GLN* 3.8 31.6 - - + -
90E TRP* 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B VAL* 3.7 22.7 - - + -
372B LEU 2.8 20.9 + - - +
373B LEU* 3.5 9.2 - - + +
375B TRP* 1.3 86.2 - - + +
377B GLY* 1.3 58.8 + - - +
378B ALA* 4.0 9.4 - - + +
589B PHE* 5.1 0.2 - - + -
608B ILE* 3.6 32.3 - - + -
609B PHE* 4.4 9.0 - - + -
619B ALA 3.6 24.0 - - - +
622B LEU* 4.3 8.7 - - + -
623B ARG* 3.4 31.1 - - + +
626B TYR* 3.5 15.0 - - + +
627B TRP* 3.6 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 4.3 0.2 - - - -
292B LEU* 3.8 12.9 - - - +
346B HIS* 3.0 30.3 + - - -
374B ARG 3.2 8.6 + - - -
375B TRP 3.1 5.7 + - - -
376B LEU* 1.3 77.7 - - - +
378B ALA* 1.3 60.6 + - - +
626B TYR* 3.6 7.4 - - - +
627B TRP* 3.3 25.6 - - - -
----------------------------------------------------------
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