Contacts of the helix formed by residues 350 - 360 (chain A) in PDB entry 3F98
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 VAL 350 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A SER* 3.5 11.1 - - - -
321A TYR* 3.8 17.5 - - + -
349A SER* 1.3 75.7 - - - +
351A HIS* 1.3 67.0 + - - +
352A GLN 3.9 6.7 - - - +
353A ASN* 2.8 37.3 + - - +
354A PHE* 4.6 1.2 - - - -
370A LYS* 3.6 29.4 - - + +
371A LEU 4.3 2.0 - - - -
372A LYS 3.8 18.4 - - - +
373A GLY* 4.2 10.3 - - - -
534A FMT 3.6 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A HIS* 2.8 30.3 + + - +
273A SER* 5.5 1.1 - - - +
296A ASP* 3.2 26.0 - - + +
319A SER* 3.5 2.4 + - - -
322A PHE* 3.8 23.3 - + + -
350A VAL* 1.3 72.0 - - - +
352A GLN* 1.3 96.2 + - + +
353A ASN 3.2 1.0 + - - -
354A PHE* 3.4 7.6 + - - -
370A LYS* 5.6 1.3 - - + -
473A NTJ 3.5 36.4 - - - +
534A FMT 2.9 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PHE* 6.1 0.5 - - - -
272A HIS* 4.7 0.7 - - - -
350A VAL* 3.1 2.2 + - - +
351A HIS* 1.3 105.6 + - + +
353A ASN* 1.3 63.4 + - - +
354A PHE 3.1 2.7 - - - -
355A ALA* 3.1 41.9 + - - +
357A PHE* 4.3 12.5 - - - +
358A THR* 3.4 5.9 + - - +
370A LYS 3.6 24.0 - - - +
371A LEU* 3.9 34.7 - - + +
473A NTJ 3.7 16.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 6.2 0.9 - - + -
349A SER* 3.2 20.6 - - - -
350A VAL* 2.8 44.0 + - - +
352A GLN* 1.3 76.8 - - - +
354A PHE* 1.3 65.8 + - + +
355A ALA 3.7 0.2 + - - -
358A THR* 3.4 29.9 + - - +
373A GLY 3.7 11.4 + - - +
375A ILE* 4.2 4.8 + - - +
377A SER* 3.6 22.9 + - - +
380A ALA* 4.0 14.6 - - + +
381A ILE* 3.5 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR* 3.5 7.5 - - - -
162A ALA* 5.8 1.2 - - - +
163A ILE* 3.3 27.3 - - + +
272A HIS* 3.5 30.7 - + + -
295A LEU* 3.9 17.3 - - + -
296A ASP* 3.8 27.1 - - + -
317A ILE* 3.5 33.7 - - + -
318A ASN 4.2 3.8 - - - -
319A SER* 4.1 10.1 - - - -
346A ILE* 4.0 13.9 - - + -
349A SER* 5.6 0.4 - - - -
350A VAL 4.6 1.3 - - - -
351A HIS 3.5 13.5 - - - -
352A GLN 3.1 1.2 - - - -
353A ASN* 1.3 83.8 - - + +
355A ALA* 1.3 58.4 + - - +
356A ASP* 5.3 0.7 - - - +
381A ILE* 4.0 10.0 - - + +
384A SER* 3.4 32.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 3.8 11.0 - - + +
160A TYR* 3.7 23.3 - - + +
162A ALA* 6.0 0.4 - - - -
272A HIS* 4.7 6.3 - - + -
351A HIS 4.6 0.2 + - - -
352A GLN* 3.1 31.4 + - - +
354A PHE* 1.3 79.7 - - - +
356A ASP* 1.3 66.3 + - - +
357A PHE* 3.2 4.6 + - + +
358A THR* 3.1 21.5 - - - +
359A PHE* 5.3 1.8 - - - -
473A NTJ 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 4.1 10.5 - - + +
97A TRP* 3.0 35.7 + - + +
158A THR 3.4 0.2 - - - +
159A LEU* 2.8 26.3 + - - +
160A TYR* 3.7 2.1 - - - -
161A SER* 2.6 36.0 + - - -
162A ALA* 2.9 30.5 + - - +
354A PHE 5.3 0.5 - - - +
355A ALA* 1.3 68.3 - - - +
357A PHE* 1.3 56.9 + - - +
358A THR 3.0 5.6 - - - -
359A PHE* 2.9 33.3 + - - +
360A ALA* 3.7 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TRP* 3.5 32.5 - + - -
98A ILE* 3.9 11.7 - - + -
104A PHE* 5.4 0.9 - + - -
107A LEU* 4.0 25.4 - - + -
121A LEU* 5.5 4.9 - - + -
125A PHE* 4.1 28.3 - + - -
159A LEU* 4.0 26.0 - - + -
352A GLN* 4.3 11.2 - - - +
355A ALA* 3.2 3.7 + - + +
356A ASP* 1.3 76.8 - - - +
358A THR* 1.3 59.8 + - - +
359A PHE 3.0 2.3 + - - -
360A ALA* 3.1 25.5 + - + +
361A THR* 4.2 2.3 + - - -
371A LEU* 3.7 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLN* 3.4 13.0 + - - +
353A ASN* 3.4 22.8 + - - +
355A ALA 3.1 19.3 + - - +
356A ASP 3.0 1.0 - - - -
357A PHE* 1.3 76.1 - - - +
359A PHE* 1.3 85.1 + - + +
361A THR* 5.1 0.4 - - - -
371A LEU* 2.7 30.8 + - - +
372A LYS* 2.8 33.1 + - - -
377A SER* 2.7 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 3.5 39.8 - - - +
56A ILE* 4.1 8.5 - - + +
57A PRO* 3.6 25.8 - - + -
162A ALA* 3.7 17.0 - - + -
355A ALA 4.7 2.7 - - - -
356A ASP* 2.9 19.1 + - - +
358A THR* 1.3 94.8 - - + +
360A ALA* 1.3 62.3 + - - +
361A THR 3.4 7.7 + - - +
372A LYS* 4.7 3.8 - - - +
377A SER* 3.6 35.7 - - - -
378A ASN* 3.7 20.2 - - - -
381A ILE* 3.9 13.9 - - + -
555A FMT 3.7 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 5.6 2.0 - - - +
97A TRP* 4.1 12.3 - - + -
125A PHE* 3.5 29.6 - - + -
128A MET* 4.4 17.3 - - - +
356A ASP 3.7 1.7 + - - +
357A PHE* 3.1 39.2 + - + +
359A PHE* 1.3 79.7 - - - +
361A THR* 1.3 61.4 + - + +
----------------------------------------------------------
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