Contacts of the helix formed by residues 85 - 96 (chain Y) in PDB entry 6QY3
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 HIS 85 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Y ASN* 4.0 23.7 + - - +
64Y LEU* 5.1 13.5 - - + -
83Y ALA 3.8 0.6 + - - -
84Y ARG* 1.3 79.8 - - - +
86Y ASP* 1.3 65.6 + - - +
87Y SER* 3.2 12.8 + - - +
88Y SER* 3.5 18.8 + - - +
89Y LEU* 4.0 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Y ARG 4.0 0.4 + - - -
85Y HIS* 1.3 72.9 - - - +
87Y SER* 1.3 59.2 + - - +
88Y SER 3.3 0.2 - - - -
89Y LEU* 3.0 13.7 + - + +
90Y GLN* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85Y HIS* 3.2 9.0 - - - +
86Y ASP* 1.3 78.3 - - - +
88Y SER* 1.3 57.3 + - - +
90Y GLN* 2.8 25.5 + - - +
91Y ILE* 2.9 14.7 + - - +
194Y VAL 5.8 1.1 - - - -
195Y CYS 4.5 4.3 - - - -
196Y GLY* 4.2 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Y ARG* 5.0 10.8 - - - -
85Y HIS* 3.5 14.3 + - - +
86Y ASP 3.3 0.6 - - - -
87Y SER* 1.3 78.5 - - - +
89Y LEU* 1.3 60.3 + - - +
90Y GLN 3.6 0.2 + - - -
91Y ILE* 3.6 17.8 + - - +
92Y ALA* 4.2 4.5 + - - +
211Z GLN* 6.0 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85Y HIS 4.0 2.1 + - - +
86Y ASP* 3.0 17.9 + - + +
88Y SER* 1.3 78.7 - - - +
90Y GLN* 1.3 60.9 + - - +
91Y ILE 3.3 0.2 - - - -
92Y ALA* 3.7 16.8 + - - +
93Y ARG* 4.4 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Y ASP 2.9 11.6 + - - +
87Y SER* 2.8 15.1 + - - +
89Y LEU* 1.3 74.5 - - - +
91Y ILE* 1.3 63.0 + - - +
92Y ALA 3.2 2.2 - - - -
93Y ARG* 3.3 18.1 + - + +
94Y GLN* 3.5 8.7 + - - +
195Y CYS 5.1 7.9 - - - +
196Y GLY 6.3 0.9 - - - -
197Y CYS* 6.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87Y SER 2.9 10.3 + - - +
88Y SER* 3.8 13.5 - - - +
89Y LEU 3.3 1.2 - - - -
90Y GLN* 1.3 74.8 - - - +
92Y ALA* 1.3 60.7 + - - +
94Y GLN* 3.0 12.7 + - + +
95Y ILE* 2.9 25.8 + - - +
196Y GLY 4.5 13.9 - - - +
197Y CYS* 5.3 4.0 - - - +
198Y MET* 5.4 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Y SER 4.2 4.6 + - - +
89Y LEU* 3.7 13.4 + - - +
90Y GLN 3.2 0.6 - - - -
91Y ILE* 1.3 79.1 - - - +
93Y ARG* 1.3 55.9 + - - +
95Y ILE* 3.2 10.6 + - - +
96Y ALA* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89Y LEU 4.4 1.7 + - - +
90Y GLN* 3.3 14.3 + - - +
91Y ILE 3.2 0.6 - - - -
92Y ALA* 1.3 75.2 - - - +
94Y GLN* 1.3 62.0 + - - +
96Y ALA* 3.0 22.3 + - - +
97Y TRP* 3.1 12.5 + - - +
277Y LEU 5.6 1.4 - - - +
278Y ASN* 4.6 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 94 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90Y GLN 3.5 4.4 + - - +
91Y ILE* 3.0 18.0 + - + +
93Y ARG* 1.3 77.9 - - - +
95Y ILE* 1.3 60.2 + - - +
96Y ALA 3.4 0.3 + - - -
97Y TRP* 3.4 19.8 + - - +
197Y CYS* 4.4 22.4 - - + -
198Y MET* 5.2 4.7 - - + +
201Y ILE* 5.5 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91Y ILE 2.9 11.7 + - - +
92Y ALA* 3.2 13.2 + - - +
94Y GLN* 1.3 76.2 - - - +
96Y ALA* 1.3 57.8 + - - +
97Y TRP 3.4 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Y ALA 3.0 14.0 + - - +
93Y ARG* 3.0 12.9 + - - +
95Y ILE* 1.3 77.7 - - - +
97Y TRP* 1.3 64.0 + - - +
98Y LYS* 3.2 5.0 + - - +
----------------------------------------------------------
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