Contacts of the helix formed by residues 84 - 94 (chain I) in PDB entry 3Q2K
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 84 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I THR* 4.3 1.8 - - - +
81I PRO* 3.0 29.9 + - + +
83I GLY* 1.3 74.7 - - - +
85I HIS* 1.3 68.5 + - - +
86I PRO* 2.9 4.7 - - - -
87I TRP* 3.1 12.5 + - + -
88I GLN* 2.8 42.4 + - + +
180I TRP* 4.0 26.2 - - + -
500I NAI 3.6 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 85 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I LEU* 3.5 21.4 + - + +
80I THR* 2.9 37.2 + - - -
81I PRO 3.4 8.7 - - - -
82I SER* 2.9 13.7 + - - +
84I LEU* 1.3 77.2 - - - +
86I PRO* 1.3 54.8 - - - +
88I GLN* 4.7 0.9 - - - +
89I ALA* 2.7 33.4 + - - +
101I SER* 3.3 11.0 + - - +
102I GLU* 2.9 40.1 + - + +
104I PRO 2.9 14.3 + - - -
105I MET 3.2 16.6 - - - +
115I MET* 4.3 0.9 - - - -
500I NAI 3.1 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 86 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I SER 3.7 2.0 - - - +
83I GLY* 3.4 17.7 - - - +
84I LEU 3.2 5.8 - - - -
85I HIS* 1.3 91.4 - - + +
87I TRP* 1.3 65.1 + - + +
89I ALA* 3.2 1.7 + - - +
90I ILE* 2.9 38.3 + - + +
105I MET 3.8 1.1 - - - +
106I ALA* 3.3 31.6 - - + -
107I THR 4.9 0.9 - - - +
111I ASP* 3.7 30.3 - - + +
114I ARG* 6.6 0.2 - - - -
115I MET* 3.7 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 87 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I GLY 3.4 24.3 + - - -
84I LEU* 3.1 13.6 + - + +
86I PRO* 1.3 79.3 - - + +
88I GLN* 1.3 65.8 + - + +
90I ILE* 3.5 9.8 + - + +
91I GLU* 3.2 22.5 + - - +
111I ASP* 3.4 35.1 + - + -
114I ARG* 3.6 41.3 - - - -
180I TRP* 5.8 2.0 - + - -
117L LYS* 4.3 27.8 - - - -
121L GLU* 5.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I VAL* 3.8 9.5 - - - +
64I LEU* 3.9 22.4 - - + +
78I LEU* 3.9 24.1 - - + +
80I THR* 2.7 36.0 + - - +
84I LEU* 2.8 30.5 + - + +
85I HIS 4.0 1.3 - - - +
87I TRP* 1.3 77.8 - - + +
89I ALA* 1.3 66.7 + - - +
90I ILE 3.1 0.3 + - - -
91I GLU* 3.2 3.0 + - - +
92I VAL* 3.0 25.6 + - - +
500I NAI 3.4 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I LEU* 3.7 8.1 - - + +
85I HIS 2.7 23.0 + - - +
86I PRO 3.9 2.0 - - - +
88I GLN* 1.3 72.8 - - - +
90I ILE* 1.3 59.1 + - - +
92I VAL* 3.2 3.0 + - - +
93I ALA* 2.8 30.5 + - - +
99I VAL* 3.9 32.1 - - + +
115I MET* 3.9 22.7 - - + -
119I CYS* 5.1 6.7 - - - -
126I LEU* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I PRO* 2.9 22.5 + - + +
87I TRP* 3.8 15.0 - - + +
88I GLN 3.1 0.2 - - - -
89I ALA* 1.3 76.9 - - - +
91I GLU* 1.3 65.4 + - - +
93I ALA* 3.1 2.4 + - - +
94I GLN* 2.9 45.0 + - - +
111I ASP 5.5 0.4 - - - +
114I ARG* 3.3 48.2 - - + +
115I MET* 3.9 9.6 - - + +
118I ALA* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I LEU* 2.8 31.7 - - + +
65I SER* 3.1 29.8 - - - -
68I LEU* 3.7 18.1 - - + +
87I TRP 3.2 13.7 + - - +
88I GLN 3.7 6.5 - - - +
90I ILE* 1.3 74.2 - - - +
92I VAL* 1.3 62.4 + - - +
94I GLN* 3.1 25.4 + - - +
95I ALA* 3.3 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I LEU* 4.2 17.7 - - + -
68I LEU* 3.9 8.7 - - + -
76I LEU* 3.7 39.0 - - + -
78I LEU* 4.6 8.3 - - + -
88I GLN 3.0 21.2 + - - +
89I ALA* 3.6 3.1 - - - +
91I GLU* 1.3 71.9 - - - +
93I ALA* 1.3 66.3 + - - +
95I ALA* 3.2 10.2 + - - +
97I ARG* 3.3 20.2 + - + +
98I HIS 3.6 13.7 - - - +
99I VAL* 3.4 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I ALA 2.8 16.0 + - - +
90I ILE 3.5 7.4 - - - +
92I VAL* 1.3 68.8 - - - +
94I GLN* 1.3 60.4 + - + +
95I ALA 2.9 5.8 - - - -
96I GLY* 2.7 19.1 + - - -
97I ARG 3.9 9.6 - - - -
99I VAL* 4.3 1.1 - - - +
118I ALA* 3.8 27.8 - - + +
119I CYS* 4.0 18.8 - - - -
122I ALA* 3.2 22.7 - - + +
124I VAL* 4.1 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 94 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I ILE* 2.9 35.3 + - + +
91I GLU* 3.1 18.2 + - + +
93I ALA* 1.3 77.2 - - + +
95I ALA* 1.3 56.6 + - - +
96I GLY 3.3 1.1 - - - -
118I ALA* 5.9 2.8 - - + +
122I ALA* 4.8 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