Contacts of the helix formed by residues 554 - 561 (chain B) in PDB entry 6GYS
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 GLU 554 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 5.3 5.9 - - - +
81B LYS 5.5 2.8 - - - +
83B ARG 5.6 1.9 - - - +
307B ARG* 4.5 19.0 - - - +
551B LYS 2.6 21.5 - - - +
552B ASN* 2.9 15.6 + - - +
553B ASP* 1.3 70.8 + - - +
555B MET* 1.3 59.9 + - - +
556B PHE 3.2 2.7 - - - +
557B SER* 2.3 49.2 + - - +
558B LEU 3.3 0.7 + - - -
267C PHE* 3.2 29.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B ASP* 3.2 27.5 + - - +
554B GLU* 1.3 78.9 - - - +
556B PHE* 1.3 62.8 + - + +
558B LEU* 3.0 33.0 + - - +
559B ILE* 2.8 39.7 + - + +
267C PHE* 4.9 11.0 - - + +
269C VAL* 3.9 28.0 - - + -
282C GLU* 4.9 17.5 - - + +
285C ALA* 5.5 1.6 - - + -
286C LYS* 5.4 14.1 - - + -
289C LEU* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B LEU* 4.2 27.1 - - + -
553B ASP* 4.3 17.5 - - - +
554B GLU* 3.2 0.8 - - - -
555B MET* 1.3 80.0 - - + +
557B SER* 1.3 60.4 + - - +
559B ILE* 3.2 25.8 + - + +
560B LYS* 2.9 40.6 + - - +
567B PRO* 4.0 18.6 - - + -
569B ASN* 3.8 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 5.8 5.8 - - - +
554B GLU* 2.3 52.1 + - - +
556B PHE* 1.3 79.2 - - - +
558B LEU* 1.3 55.2 + - - +
560B LYS* 3.4 9.2 + - - +
561B GLY 2.9 22.9 + - - -
230C ASP* 3.4 18.3 - - - +
267C PHE* 3.5 8.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B GLU 4.0 4.5 - - - +
555B MET* 3.0 30.8 + - - +
557B SER* 1.3 79.3 + - - +
559B ILE* 1.3 60.7 + - - +
561B GLY* 3.3 1.9 + - - +
562B LEU* 2.9 44.3 + - + +
230C ASP* 4.3 7.9 - - - -
231C ILE* 4.9 9.8 - - + +
267C PHE* 3.8 32.5 - - + -
285C ALA* 3.7 28.3 - - + -
289C LEU* 3.7 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B MET* 2.8 28.9 + - + +
556B PHE* 3.3 35.2 - - + +
558B LEU* 1.3 78.5 - - + +
560B LYS* 1.3 59.0 + - + +
562B LEU* 3.0 23.3 + - - +
563B GLY 3.1 9.5 - - - +
565B LEU* 3.3 27.5 + - - +
567B PRO* 3.7 26.5 - - + -
279C ASP* 5.0 2.5 - - + +
281C VAL* 3.7 20.1 - - + +
282C GLU* 5.0 10.1 - - + -
285C ALA* 4.9 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 5.3 7.3 + - - -
86B THR* 6.0 5.6 - - + -
87B ARG* 5.8 3.4 - - - +
556B PHE* 2.9 27.0 + - - +
557B SER* 3.8 7.6 - - - +
559B ILE* 1.3 78.5 - - + +
561B GLY* 1.3 56.6 + - - +
563B GLY* 2.9 20.5 + - - +
564B SER* 5.1 1.7 - - - +
565B LEU 5.5 0.9 - - - +
567B PRO* 5.9 6.5 - - + -
155C ASP* 4.0 7.1 - - - +
159C TRP* 4.7 2.1 - - - -
232C ARG* 4.0 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B SER 2.9 14.5 + - - -
558B LEU* 3.3 6.3 + - - -
559B ILE 3.2 0.4 - - - -
560B LYS* 1.3 73.4 - - - +
562B LEU* 1.3 63.5 + - - +
563B GLY 3.2 6.3 + - - -
159C TRP* 4.7 3.7 - - - -
230C ASP* 3.9 4.0 - - - -
231C ILE* 4.0 6.1 - - - +
232C ARG* 3.2 43.6 - - - -
235C GLN* 4.4 4.3 - - - +
----------------------------------------------------------
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