Contacts of the helix formed by residues 80 - 98 (chain H) in PDB entry 3SZ9
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 ASP 80 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E ASP* 3.4 35.8 - - - +
148E GLY* 2.8 15.2 + - - -
498E LYS* 2.8 32.8 + - - +
127F LYS* 5.6 1.4 + - - -
78H ARG 3.3 2.1 + - - +
79H MET* 1.3 76.3 - - - +
81H ALA* 1.3 66.6 + - - +
82H SER* 3.8 6.5 - - - +
83H HIS* 2.9 21.3 + - + +
84H ARG* 3.2 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E PRO* 3.9 26.3 + - + +
498E LYS* 4.9 3.2 - - - +
79H MET 3.3 2.8 + - - -
80H ASP* 1.3 70.9 - - - +
82H SER* 1.3 63.7 + - - +
84H ARG* 3.1 34.3 + - - +
85H GLY 3.3 8.0 + - - -
136H ALA* 3.3 32.8 - - - +
137H ASP* 3.8 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E PRO 5.1 0.2 + - - -
147E ASP* 2.6 34.2 + - - -
127F LYS* 5.6 4.5 - - - +
462F GLN* 3.7 7.6 - - - +
80H ASP* 3.8 3.2 - - - +
81H ALA* 1.3 78.0 - - - +
83H HIS* 1.3 60.1 + - - +
85H GLY* 3.2 4.5 + - - +
86H ARG* 3.1 29.4 + - - +
136H ALA* 5.1 0.4 - - - -
137H ASP* 3.5 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H MET* 3.6 33.7 - - + +
80H ASP* 2.9 19.5 + - + +
82H SER* 1.3 78.2 + - - +
84H ARG* 1.3 60.5 + - - +
85H GLY 3.2 1.1 - - - -
86H ARG* 3.3 19.3 + - + +
87H LEU* 2.9 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E PRO* 5.9 0.6 - - - +
500E SER* 3.9 24.9 - - - -
76H TRP* 3.7 32.5 + - + -
79H MET* 4.0 18.6 + - + -
80H ASP 3.2 8.5 + - - +
81H ALA* 3.1 28.3 + - - +
83H HIS* 1.3 76.7 - - - +
85H GLY* 1.3 58.3 + - - +
87H LEU* 3.3 6.1 + - - +
88H LEU* 3.0 32.1 + - - +
136H ALA* 3.1 21.7 + - + -
183H LEU 3.4 17.7 + - - +
184H ALA* 2.8 29.7 + - - -
185H THR* 3.8 9.8 + - - +
186H GLY* 3.4 18.7 - - - +
213H PHE* 4.9 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H ALA 3.3 4.6 + - - -
82H SER* 3.2 7.9 + - - -
83H HIS 3.2 0.6 - - - -
84H ARG* 1.3 77.5 - - - +
86H ARG* 1.3 58.4 + - - +
88H LEU* 3.3 1.4 + - - -
89H ASN* 2.9 30.0 + - - -
133H ALA* 3.4 37.6 - - - +
136H ALA* 3.6 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F ASN* 5.0 3.2 + - - -
93F ASP* 4.6 4.0 + - - -
96F GLU* 4.8 2.0 + - - -
130F ARG* 3.3 63.9 - - - +
82H SER* 3.1 17.7 + - - +
83H HIS* 3.3 27.3 + - + +
85H GLY* 1.3 74.8 - - - +
87H LEU* 1.3 54.3 + - + +
89H ASN* 3.2 23.1 + - - +
90H ARG* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H TRP* 4.1 3.1 - - + -
79H MET* 3.7 37.0 - - + -
83H HIS* 2.9 32.6 + - + +
84H ARG 3.7 2.7 - - - +
86H ARG* 1.3 72.7 - - + +
88H LEU* 1.3 61.1 + - - +
90H ARG* 3.4 6.6 + - + +
91H LEU 2.9 23.7 + - - -
211H ALA* 3.3 26.4 - - - +
212H GLY* 4.2 16.4 - - - +
213H PHE* 3.5 43.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H ARG 3.0 19.1 + - - +
85H GLY* 3.7 6.7 - - - +
87H LEU* 1.3 76.3 - - - +
89H ASN* 1.3 58.0 + - - +
91H LEU* 3.3 6.7 + - + +
92H ALA* 3.0 27.2 + - - +
129H LEU* 4.1 35.9 - - + +
132H TYR* 4.9 0.2 - - + -
133H ALA* 3.7 30.1 - - + +
180H GLY* 4.0 11.7 - - - +
183H LEU* 4.1 27.8 - - + -
184H ALA* 3.8 31.6 - - + +
213H PHE* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ARG* 5.1 2.7 + - - -
89F ASN* 4.4 21.6 + - - +
85H GLY 2.9 21.4 + - - +
86H ARG* 3.2 25.7 + - - +
88H LEU* 1.3 75.0 - - - +
90H ARG* 1.3 64.8 + - - +
92H ALA* 3.3 4.4 + - - +
93H ASP* 3.0 31.8 + - - +
130H ARG* 3.4 27.6 + - - +
133H ALA* 3.6 18.4 - - - +
134H GLY 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H ARG 2.8 20.3 + - - +
87H LEU* 3.6 9.9 - - + +
89H ASN* 1.3 73.8 - - - +
91H LEU* 1.3 57.0 + - - +
93H ASP* 3.1 25.0 + - - +
94H LEU* 2.9 62.3 + - + +
97H ARG* 5.3 1.0 - - - +
210H GLU* 4.9 6.9 + - - +
211H ALA* 3.9 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H LEU 2.9 17.1 + - - +
88H LEU* 3.6 7.9 - - + +
90H ARG* 1.3 77.0 - - - +
92H ALA* 1.3 57.6 + - - +
94H LEU* 3.2 2.7 + - - +
95H ILE* 2.9 37.6 + - + +
129H LEU* 4.1 29.2 - - + -
179H LEU* 5.2 5.6 - - + -
183H LEU* 5.4 2.0 - - + -
204H VAL* 4.4 6.3 - - + -
207H LEU* 3.8 28.5 - - + -
208H ILE* 3.9 35.0 - - + +
211H ALA* 4.0 6.7 - - + +
213H PHE* 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H LEU 3.0 17.0 + - - +
89H ASN 3.8 3.4 - - - +
90H ARG 3.3 0.2 - - - -
91H LEU* 1.3 77.2 - - - +
93H ASP* 1.3 53.4 + - - +
95H ILE* 3.4 3.3 + - - -
96H GLU* 2.8 30.1 + - - +
126H LEU* 2.9 23.0 - - + +
129H LEU* 4.2 19.0 - - + +
130H ARG* 3.7 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ARG* 4.6 4.0 + - - -
93F ASP* 5.4 4.0 - - - +
89H ASN* 3.0 20.8 + - - +
90H ARG* 3.1 27.7 + - - +
92H ALA* 1.3 75.0 - - - +
94H LEU* 1.3 58.0 + - - +
96H GLU* 3.4 3.8 + - - +
97H ARG* 3.0 27.4 + - - +
130H ARG* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H ARG* 2.9 46.0 + - - +
91H LEU* 3.2 6.9 + - - +
93H ASP* 1.3 73.4 - - - +
95H ILE* 1.3 66.4 + - - +
97H ARG* 3.6 33.5 + - - +
98H ASP* 3.3 27.4 + - - +
207H LEU* 3.4 41.3 - - + +
210H GLU* 3.7 17.9 - - + +
211H ALA* 3.4 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H LEU* 2.9 28.7 + - + +
92H ALA 3.6 3.8 - - - +
94H LEU* 1.3 76.6 - - - +
96H GLU* 1.3 57.6 + - - +
98H ASP* 3.2 5.0 + - - +
99H ARG* 3.0 24.4 + - - -
102H LEU* 4.2 10.9 - - + +
122H LEU* 3.8 24.9 - - + -
125H VAL* 4.0 15.9 - - + -
126H LEU* 3.8 14.4 - - + -
129H LEU* 3.5 31.6 - - + -
172H LEU* 6.1 0.2 - - + -
204H VAL* 4.4 17.5 - - + -
207H LEU* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ARG* 4.7 2.1 + - - -
92H ALA 2.8 20.0 + - - +
93H ASP* 3.4 5.6 + - - +
94H LEU 3.3 0.2 - - - -
95H ILE* 1.3 71.2 - - - +
97H ARG* 1.3 65.9 + - - +
99H ARG* 3.1 33.4 + - - +
126H LEU* 3.8 22.0 - - + -
130H ARG* 2.8 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H ARG* 5.3 1.2 - - - +
93H ASP 3.0 17.5 + - - +
94H LEU* 3.6 20.8 + - - +
96H GLU* 1.3 76.0 - - - +
98H ASP* 1.3 90.7 + - - +
99H ARG 3.5 1.9 + - - -
100H THR 5.1 1.0 + - - -
203H TYR* 4.6 2.0 + - - -
207H LEU* 3.8 7.1 - - - +
210H GLU* 2.9 38.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H LEU 3.3 8.6 + - - +
95H ILE 3.2 7.1 + - - +
96H GLU 3.2 0.8 - - - -
97H ARG* 1.3 113.4 + - - +
99H ARG* 1.3 57.9 + - - +
100H THR 3.4 3.1 + - - -
101H TYR* 3.4 5.7 + - + -
102H LEU* 2.9 32.5 + - + +
203H TYR* 2.8 41.3 + - + -
207H LEU* 3.7 5.2 - - + +
6921H EDO 4.0 17.0 + - - -
----------------------------------------------------------
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