Contacts of the helix formed by residues 84 - 94 (chain H) in PDB entry 5A31
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 LYS 84 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H TYR* 3.0 42.2 + - + +
79H CYS* 2.9 17.9 + - + +
82H LEU* 3.8 27.1 - - + +
83H SER* 1.3 75.9 - - - +
85H LEU* 1.3 63.2 + - - +
86H ALA* 3.2 4.5 - - + -
87H GLU* 3.1 30.4 + - + +
88H GLY 3.1 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H VAL* 4.0 39.7 - - + +
83H SER* 3.1 15.0 + - - +
84H LYS* 1.3 73.6 - - - +
86H ALA* 1.3 62.6 + - - +
88H GLY* 3.5 0.7 + - - -
89H GLU* 3.1 24.3 + - - +
123H HIS* 5.5 0.4 - - + -
124H VAL* 3.8 26.2 - - + +
127H LYS* 3.8 45.1 - - + +
128H THR* 4.8 7.2 - - - +
473K VAL* 4.5 4.9 - - + +
476K PRO* 4.5 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H LYS 3.2 0.9 - - - -
85H LEU* 1.3 79.6 - - - +
87H GLU* 1.3 61.5 + - - +
89H GLU* 3.4 3.6 + - - +
90H GLN* 3.2 23.2 + - - +
441K VAL* 3.7 32.8 - - + -
473K VAL* 3.3 39.8 + - + +
474K LEU* 3.8 6.2 - - + +
476K PRO* 5.4 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H TYR* 2.4 49.0 + - - -
62H LYS* 3.2 26.7 + - - +
75H LEU* 4.5 4.0 - - - +
79H CYS* 3.6 8.1 - - - -
84H LYS* 3.1 30.2 + - + +
86H ALA* 1.3 77.2 - - + +
88H GLY* 1.3 64.7 + - - +
90H GLN* 3.3 20.8 - - + +
91H ILE* 3.3 21.1 - - + +
439K VAL* 5.1 7.2 - - + -
441K VAL* 5.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H ALA* 3.7 21.7 - - - +
79H CYS* 3.4 25.4 - - - +
80H VAL* 5.0 4.5 - - - -
84H LYS 3.1 11.6 + - - -
85H LEU 3.9 2.9 - - - -
87H GLU* 1.3 78.6 - - - +
89H GLU* 1.3 61.6 + - - +
90H GLN 3.5 0.2 + - - -
91H ILE* 3.6 9.3 + - - +
92H LEU* 3.6 11.4 + - - +
124H VAL* 5.3 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H LEU 3.1 17.5 + - - +
86H ALA 3.6 5.6 - - - +
87H GLU 3.3 0.2 - - - -
88H GLY* 1.3 77.0 - - - +
90H GLN* 1.3 56.7 + - - +
91H ILE 3.3 0.2 + - - -
92H LEU* 3.4 1.8 + - - +
93H SER* 2.5 52.7 + - - +
95H GLY* 4.6 6.0 - - - +
96H VAL* 4.6 10.7 - - + +
121H LEU* 4.3 10.3 - - + +
124H VAL* 4.0 14.4 - - + +
125H TYR* 3.7 10.7 + - - -
130H ARG* 2.7 31.4 + - - -
133H LYS* 5.3 2.1 + - - -
473K VAL* 3.0 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H ALA 3.2 10.8 + - - +
87H GLU* 3.3 20.0 - - + +
89H GLU* 1.3 79.4 - - - +
91H ILE* 1.3 70.6 + - - +
93H SER* 3.8 4.9 - - - -
94H GLY* 2.6 31.7 + - - -
95H GLY 3.8 18.8 - - - +
96H VAL* 4.9 5.3 + - + +
98H ASN* 4.1 24.4 + - - +
439K VAL* 3.2 44.9 - - + +
441K VAL* 6.0 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H LYS* 3.5 52.3 - - + +
75H LEU* 3.5 38.6 - - + -
76H ALA* 4.2 5.4 - - + +
79H CYS* 3.8 13.7 - - - -
87H GLU* 3.3 24.5 - - + +
88H GLY 3.9 6.3 - - - +
89H GLU 3.2 0.4 - - - -
90H GLN* 1.3 90.4 - - - +
92H LEU* 1.3 62.5 + - - +
101H LYS* 3.3 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H LYS 4.5 2.5 - - - +
73H TYR* 4.5 6.3 - - + -
76H ALA* 3.4 32.8 - - + -
88H GLY 3.6 6.7 + - - +
89H GLU* 3.4 2.8 + - - +
91H ILE* 1.3 79.1 - - - +
93H SER* 1.3 60.2 + - - +
101H LYS* 2.8 24.3 + - - +
106H ILE* 4.0 12.6 - - + +
110H PHE* 3.4 38.8 - - + -
117H THR* 4.2 24.9 - - + +
120H LEU* 3.8 24.0 - - + -
121H LEU* 3.9 21.5 - - + +
124H VAL* 5.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H GLU* 2.5 38.2 + - - +
92H LEU* 1.3 79.9 - - - +
94H GLY* 1.3 59.1 + - - +
95H GLY* 2.8 25.2 + - - -
100H GLN* 6.4 0.2 - - - -
101H LYS* 3.0 34.2 + - - +
106H ILE* 4.6 7.9 - - - -
121H LEU* 4.0 17.3 - - - -
125H TYR* 4.3 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H GLN 2.6 24.5 + - - -
92H LEU 3.4 1.6 + - - -
93H SER* 1.3 72.9 - - - +
95H GLY* 1.3 51.8 + - - +
98H ASN* 3.0 37.2 - - - +
99H LYS 2.5 21.7 - - - +
101H LYS* 3.7 13.4 - - - +
----------------------------------------------------------
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