Contacts of the helix formed by residues 388 - 401 (chain B) in PDB entry 4U7C
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 388 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B PHE* 1.3 77.4 - - - +
389B GLU* 1.3 67.0 + - - +
390B THR* 3.8 1.9 + - - -
391B SER* 3.2 10.6 + - - -
392B TRP* 3.0 22.8 + - - -
12T C 2.1 47.6 + - - -
13T G 5.1 8.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B SER* 1.3 74.1 - - - +
390B THR* 1.3 58.6 + - - +
392B TRP* 3.4 16.1 + - + +
393B HIS* 2.9 67.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B SER* 3.3 1.1 + - - -
389B GLU* 1.3 79.0 + - - +
391B SER* 1.3 59.2 + - - +
393B HIS* 3.7 6.9 - - + +
394B TYR* 2.9 32.5 + - + +
11T C 3.8 30.0 + - - +
12T C 3.8 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B PHE* 3.8 27.5 - - - -
388B SER* 3.2 13.3 + - - -
390B THR* 1.3 80.9 - - - +
392B TRP* 1.3 57.8 + - - +
394B TYR* 3.5 7.0 - - - +
395B PHE* 2.9 40.6 + - - -
11T C 6.0 0.3 - - - -
12T C 3.6 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLN* 5.7 1.1 - - + -
86B VAL* 4.1 24.0 - - + -
89B PHE* 4.0 26.9 - + + -
380B ARG* 5.0 4.5 - - + +
383B LEU* 3.7 27.6 - - + +
384B SER* 3.6 35.9 + - - +
387B PHE* 3.8 6.9 + - + -
388B SER 3.0 28.4 + - - +
389B GLU* 3.4 18.5 - - + +
391B SER* 1.3 77.2 - - - +
393B HIS* 1.3 92.9 + + - +
395B PHE* 3.6 10.0 - - + +
396B LEU* 2.9 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 3.6 35.0 - + - -
389B GLU* 2.9 48.8 + - + +
390B THR* 3.7 7.0 - - - +
392B TRP* 1.3 115.4 - + - +
394B TYR* 1.3 60.0 + - - +
396B LEU* 3.1 6.2 + - - +
397B HIS* 2.8 41.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B MET* 5.8 0.2 - - - +
354B VAL* 4.4 2.3 - - - +
355B SER 2.4 32.9 + - - -
356B GLY* 3.5 9.0 - - - -
357B ILE* 3.9 23.0 + - + -
390B THR* 2.9 19.6 + - + +
391B SER* 3.5 6.7 - - - +
393B HIS* 1.3 76.6 - - - +
395B PHE* 1.3 75.6 + + - +
397B HIS* 3.1 12.9 + - + +
398B ILE* 2.9 53.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ILE* 3.6 28.3 - - + -
361B THR* 3.9 12.3 - - + -
365B LEU* 3.8 33.0 - - + -
376B LEU* 3.3 32.3 - - + +
383B LEU* 4.3 22.7 - - + -
387B PHE* 4.2 26.7 - + - -
391B SER* 2.9 30.6 + - - +
392B TRP* 3.6 11.4 - - + +
393B HIS 3.3 0.2 - - - -
394B TYR* 1.3 83.7 - + - +
396B LEU* 1.3 58.5 - - - +
398B ILE* 3.3 3.0 + - + -
399B SER* 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 4.4 5.2 - - + +
89B PHE* 3.6 31.2 - - + -
90B ALA* 3.8 27.6 - - + +
93B LEU* 3.8 11.0 - - + -
376B LEU 5.8 0.2 - - - +
377B TYR* 4.2 18.2 - - + -
380B ARG* 4.4 18.8 - - + -
392B TRP* 2.9 29.4 + - + +
393B HIS 3.1 4.9 + - - +
395B PHE* 1.3 72.7 - - - +
397B HIS* 1.3 67.4 + - - +
399B SER* 3.0 15.6 + - - +
400B LEU* 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 4.5 9.4 - + - -
93B LEU* 3.5 32.5 - - + +
393B HIS* 2.8 34.9 + + + -
394B TYR* 3.3 13.1 + - + +
396B LEU* 1.3 76.4 - - - +
398B ILE* 1.3 65.3 + - + +
400B LEU* 3.7 1.2 - - - -
401B GLY 3.0 3.6 + - - -
402B LEU* 3.0 62.2 + - + +
403B GLY* 5.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B MET* 4.0 23.1 - - + +
346B ILE* 3.9 7.3 - - - +
349B LEU* 6.3 0.4 - - + -
351B ILE* 5.7 0.2 - - + -
354B VAL* 3.7 41.5 - - + -
357B ILE* 5.7 1.1 - - + -
373B CYS* 3.9 24.5 - - - -
376B LEU* 4.0 11.7 - - + -
394B TYR* 2.9 53.6 + - + +
395B PHE* 3.4 9.4 - - + +
397B HIS* 1.3 79.7 - - + +
399B SER* 1.3 57.6 + - - +
401B GLY* 3.1 17.8 + - - -
402B LEU 5.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B MET* 5.0 3.6 - - - +
346B ILE* 4.2 13.9 - - - +
373B CYS* 3.6 28.2 - - - +
376B LEU* 4.0 8.2 + - - -
377B TYR* 3.6 28.6 - - - +
395B PHE 2.9 13.8 + - - -
396B LEU* 3.0 29.8 + - - +
398B ILE* 1.3 75.6 - - - +
400B LEU* 1.3 63.2 + - - +
401B GLY 3.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 4.0 20.0 - - + +
93B LEU* 3.9 35.7 - - + -
94B GLU* 4.2 21.3 - - + +
97B ARG* 2.8 27.9 + - - +
339B ARG* 5.8 0.9 - - - +
343B MET* 3.3 14.2 - - + +
346B ILE* 3.9 4.7 - - - -
377B TYR* 3.9 27.1 - - + -
396B LEU* 2.9 20.1 + - + +
397B HIS* 4.0 1.3 - - - +
399B SER* 1.3 80.5 - - - +
401B GLY* 1.3 57.7 + - - +
402B LEU* 3.8 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ARG* 4.8 2.2 + - - -
316B ASN* 2.9 21.7 + - - -
318B MET* 3.9 10.1 - - - -
319B LEU* 3.7 9.3 - - - +
342B VAL* 4.2 7.9 - - - +
346B ILE* 3.3 22.1 - - - +
397B HIS 3.0 3.6 + - - -
398B ILE 3.1 9.2 + - - -
400B LEU* 1.3 78.9 - - - +
402B LEU* 1.3 61.8 + - - +
----------------------------------------------------------
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