Contacts of the helix formed by residues 544 - 559 (chain A) in PDB entry 1H3N
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 LEU 544 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLU* 3.3 43.5 - - + +
170A GLN* 4.0 5.6 - - + -
177A TRP* 4.5 17.0 - - + -
501A PHE* 3.9 31.4 - - + -
540A GLU 4.0 16.6 - - - +
541A HIS* 3.1 14.0 + - + +
543A VAL* 1.3 84.5 - - + +
545A HIS* 1.3 68.5 + - - +
546A LEU 3.3 0.2 - - - -
547A LEU 2.9 3.8 + - - -
548A TYR* 2.9 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 4.3 7.4 - - + -
501A PHE* 3.9 11.2 - - + -
504A SER* 3.0 30.1 + - - -
505A SER* 4.7 1.2 + - - -
507A TYR* 3.8 5.6 - + - -
508A TYR* 4.7 0.2 - + - -
535A TYR* 2.6 41.4 + + - -
541A HIS* 3.5 21.0 + - + +
544A LEU* 1.3 79.3 - - - +
546A LEU* 1.3 65.0 + - + +
548A TYR* 4.3 3.8 - - - -
549A SER* 2.8 63.0 + - - -
568A PHE* 4.1 3.7 - + - -
1815A LEU* 3.5 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 4.0 22.4 - - + -
212A TRP* 3.7 9.7 - - + -
216A VAL* 4.3 9.0 - - + -
220A GLN* 3.1 14.0 + - - +
535A TYR* 4.0 20.0 - - + -
538A GLY 4.5 4.7 - - - +
539A VAL 5.3 0.7 - - - +
541A HIS* 3.0 37.8 + - + +
542A ALA* 3.7 14.4 - - - +
545A HIS* 1.3 78.2 - - + +
547A LEU* 1.3 55.6 + - - +
549A SER* 4.5 2.5 - - - -
550A ARG* 3.2 23.7 - - - +
568A PHE* 4.3 7.7 - - + -
571A LEU* 3.9 32.8 - - + -
573A THR* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLU* 4.9 3.6 - - + +
196A ILE* 4.3 12.8 - - + -
203A LEU* 4.3 19.6 - - + +
220A GLN* 3.6 23.5 - - + +
223A TRP* 3.7 32.3 - - + +
224A ILE* 4.6 14.1 - - + -
419A LEU* 4.4 11.9 - - + -
542A ALA 4.0 0.4 + - - -
543A VAL* 3.8 22.0 - - + +
544A LEU 2.9 8.1 + - - +
546A LEU* 1.3 78.4 - - - +
548A TYR* 1.3 68.6 + - + +
549A SER 3.2 1.3 - - - -
550A ARG* 3.1 23.0 + - - +
551A PHE* 3.2 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA* 3.7 6.4 - - - +
169A GLU* 2.7 47.2 + - + +
170A GLN* 4.9 0.9 - - - +
196A ILE* 4.4 11.2 - - + -
422A TRP* 3.4 53.3 + + + -
501A PHE* 3.6 38.4 - + + -
505A SER* 3.3 17.3 - - - +
543A VAL 4.8 0.2 - - - -
544A LEU* 2.9 37.6 + - + +
545A HIS* 4.0 2.9 - - - +
547A LEU* 1.3 78.0 - - + +
549A SER* 1.3 58.2 + - - +
551A PHE* 3.2 10.2 + - - +
552A PHE* 3.0 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A SER 3.7 0.3 + - - -
505A SER* 3.7 17.5 - - - +
508A TYR* 3.2 20.8 + - - -
545A HIS* 2.8 47.6 + - - -
546A LEU 4.8 0.7 - - - -
548A TYR* 1.3 73.9 - - - +
550A ARG* 1.3 66.8 + - - +
552A PHE* 3.3 0.9 + - - +
553A THR* 3.0 21.0 + - - -
567A PRO* 4.4 1.1 - - - -
568A PHE* 3.8 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 2.8 58.9 + - + +
206A ASP* 3.7 16.8 - - - +
207A LEU* 3.6 12.3 - - - +
210A LEU* 4.1 2.4 - - - +
212A TRP* 3.7 19.7 - - + -
220A GLN* 2.8 28.3 + - - -
224A ILE* 5.2 0.8 - - - +
546A LEU 3.2 24.0 - - - +
547A LEU* 3.1 9.9 + - - +
549A SER* 1.3 77.3 - - - +
551A PHE* 1.3 57.4 + - - +
553A THR* 3.4 1.7 + - - -
554A LYS* 3.0 35.4 + - + +
565A GLU 4.4 0.5 - - - +
566A GLU* 2.9 42.5 + - - +
567A PRO* 4.1 16.4 - - + -
568A PHE* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET* 4.1 26.9 - - + -
148A LEU* 4.6 10.8 - - + -
194A LEU* 4.1 22.4 - - + -
195A ARG 4.4 4.7 - - - -
196A ILE* 3.7 48.5 - - + -
199A TYR* 3.6 40.2 - + + -
203A LEU* 4.0 9.5 - - + +
422A TRP* 4.1 15.0 - + - -
547A LEU 3.2 3.4 + - - +
548A TYR 3.2 8.4 + - - +
550A ARG* 1.3 79.1 - - - +
552A PHE* 1.3 72.9 + + - +
554A LYS* 3.2 5.9 + - - +
555A PHE* 2.9 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 3.9 17.9 - - + -
143A MET* 3.9 17.3 - - + -
194A LEU* 4.3 2.0 - - + -
422A TRP* 3.5 25.4 - + - -
502A PHE* 3.6 49.6 - + - -
505A SER* 3.4 38.6 - - - +
506A TRP* 3.9 27.6 - + + -
508A TYR* 4.6 0.2 - - - +
548A TYR 3.0 13.1 + - - +
549A SER 3.3 2.0 + - - +
551A PHE* 1.3 84.0 - + - +
553A THR* 1.3 57.6 + - - +
555A PHE* 3.3 6.4 + - - +
556A LEU* 2.9 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A TYR* 2.8 28.6 + - - -
509A LEU* 4.6 3.8 - - + +
530A MET* 5.0 1.7 - - + +
549A SER 3.0 11.3 + - - -
550A ARG 3.8 1.3 - - - -
552A PHE* 1.3 74.4 - - - +
554A LYS* 1.3 62.2 + - - +
556A LEU* 3.4 8.2 + - - +
557A HIS* 2.9 27.9 + - - +
562A VAL* 4.5 12.3 - - + +
564A VAL* 3.9 11.2 - - + +
565A GLU 3.8 17.0 - - - -
566A GLU 4.0 1.1 - - - +
567A PRO* 3.2 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TYR* 3.6 28.7 - - + -
202A ARG* 3.6 36.7 + - + +
203A LEU* 3.9 19.0 - - + +
206A ASP* 2.9 25.5 + - - -
550A ARG* 3.0 19.5 + - - +
551A PHE* 3.7 1.8 - - - +
553A THR* 1.3 75.9 - - - +
555A PHE* 1.3 58.8 + - - +
557A HIS* 3.3 6.8 + - - +
558A ASP* 2.9 33.8 + - - +
565A GLU* 2.8 32.1 + - + +
566A GLU* 2.6 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 4.4 8.1 - - + -
142A LYS* 3.7 26.7 - - + -
143A MET* 3.6 39.3 - - + -
146A LYS* 4.1 17.9 - - + -
148A LEU* 3.3 30.7 - - + -
199A TYR* 3.5 17.9 - - + +
551A PHE* 2.9 20.6 + - + +
552A PHE* 3.6 4.7 - - - +
554A LYS* 1.3 78.7 - - - +
556A LEU* 1.3 73.4 + - + +
558A ASP* 3.1 6.6 + - + +
559A LEU* 3.0 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TRP* 5.2 0.9 - - + -
139A ILE* 4.5 24.0 - - + -
506A TRP* 4.5 12.1 - - + -
509A LEU* 3.5 30.5 - - + -
520A PRO* 6.2 0.2 - - + -
521A PHE* 4.0 13.2 - - + -
552A PHE* 2.9 26.2 + - + +
553A THR 3.9 2.0 - - - +
555A PHE* 1.3 85.8 - - + +
557A HIS* 1.3 60.1 + - - +
559A LEU* 3.2 28.0 + - + +
561A MET* 3.0 38.4 + - + +
562A VAL* 3.5 16.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ARG* 4.9 0.2 - - - -
553A THR 2.9 17.6 + - - +
554A LYS* 3.4 6.9 + - - +
556A LEU* 1.3 77.9 - - - +
558A ASP* 1.3 69.4 + - - +
560A GLY* 2.7 25.6 + - - -
562A VAL* 2.9 33.0 - - - +
563A LYS* 3.0 22.1 + - - -
564A VAL 3.5 9.6 - - - +
565A GLU* 3.6 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TYR* 2.7 23.4 + - - +
202A ARG* 2.9 37.1 + - - -
554A LYS 2.9 13.9 + - - +
555A PHE* 3.4 10.1 - - + +
557A HIS* 1.3 85.8 + - - +
559A LEU* 1.3 60.8 + - - +
560A GLY* 3.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TRP* 4.5 3.1 - - + -
142A LYS* 4.0 27.8 - - + -
146A LYS* 4.2 24.9 - - + -
555A PHE* 3.0 47.3 + - + +
556A LEU* 3.4 18.6 - - + +
557A HIS 3.1 0.6 - - - -
558A ASP* 1.3 76.7 - - - +
560A GLY* 1.3 59.6 + - - +
561A MET* 3.7 26.7 + - + +
----------------------------------------------------------
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