Contacts of the helix formed by residues 79 - 95 (chain H) in PDB entry 3SRF
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 THR 79 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H GLY* 1.3 75.0 - - - -
80H HIS* 1.3 65.5 + - - +
81H GLU* 3.7 12.1 + - - +
82H TYR* 3.3 23.7 + - - +
83H HIS* 3.2 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H PHE* 4.5 8.9 - + - -
78H GLY 5.3 2.2 - - - -
79H THR* 1.3 74.9 - - - +
81H GLU* 1.3 65.3 + - - +
83H HIS* 3.5 2.8 + - - +
84H ALA* 3.0 20.6 + - - +
226H GLN* 3.2 37.8 - - + +
227H ASP* 2.8 24.8 + - - -
230H PHE* 3.0 49.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H THR* 3.3 9.9 + - - +
80H HIS* 1.3 78.5 - - - +
82H TYR* 1.3 61.5 + - - +
84H ALA* 3.4 6.5 + - - +
85H GLU* 3.1 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ILE 5.4 5.4 - - - -
51H GLY* 3.9 4.9 - - - -
52H PRO* 3.9 25.8 - - - +
55H ARG* 2.8 58.0 + - - +
77H HIS 6.2 0.2 - - - -
78H GLY* 4.5 9.4 - - - -
79H THR* 3.3 24.4 + - - +
80H HIS 3.3 0.2 - - - -
81H GLU* 1.3 80.0 - - - +
83H HIS* 1.3 77.9 + + - +
85H GLU* 4.7 0.9 - - - -
86H THR* 2.7 38.2 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
73H LEU* 3.4 30.4 - - + +
74H ASN 3.2 32.3 + - - -
75H PHE* 3.6 39.4 - + + -
77H HIS 3.0 21.5 + - - -
78H GLY* 3.8 6.2 + - - -
79H THR 3.2 23.3 + - - +
80H HIS 4.0 3.6 - - - +
81H GLU 3.4 0.2 - - - -
82H TYR* 1.3 92.2 - + - +
84H ALA* 1.3 61.1 + - - +
86H THR* 3.3 4.3 + - - -
87H ILE* 2.9 28.3 + - - +
230H PHE* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H HIS 3.0 19.5 + - - +
81H GLU* 3.7 6.7 - - - +
83H HIS* 1.3 75.1 - - - +
85H GLU* 1.3 59.1 + - - +
87H ILE* 3.4 4.0 + - - +
88H LYS* 2.9 29.1 + - - +
230H PHE* 3.9 5.6 - - + -
234H GLN* 3.8 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ARG* 2.8 38.8 + - - +
81H GLU* 3.1 17.7 + - + +
82H TYR* 5.0 0.9 - - - -
83H HIS 3.3 0.2 - - - -
84H ALA* 1.3 74.7 - - - +
86H THR* 1.3 63.4 + - - +
88H LYS* 3.5 12.7 + - + +
89H ASN* 3.1 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ILE* 3.7 38.1 - - + +
55H ARG* 2.9 26.0 + - + +
60H LEU* 6.0 0.2 - - + -
73H LEU* 4.2 15.3 - - + -
82H TYR* 2.7 30.9 + - + -
83H HIS* 3.5 11.0 - - - +
85H GLU* 1.3 75.9 - - - +
87H ILE* 1.3 61.9 + - - +
89H ASN* 3.2 8.8 + - - +
90H VAL* 3.1 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H LEU* 3.7 20.4 - - + -
75H PHE* 5.8 2.0 - - + -
83H HIS 2.9 21.9 + - - +
84H ALA 3.7 3.6 - - - +
86H THR* 1.3 72.6 - - - +
88H LYS* 1.3 64.6 + - - +
90H VAL* 3.4 8.8 + - - +
91H ARG* 3.1 65.2 + - + +
109H VAL* 3.9 22.8 - - + +
111H LEU* 6.3 0.4 - - + -
230H PHE* 4.7 5.8 - - + -
234H GLN* 3.9 34.8 - - + +
236H VAL* 4.6 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H ALA 2.9 17.1 + - - +
85H GLU* 3.6 12.6 - - + +
87H ILE* 1.3 77.1 - - - +
89H ASN* 1.3 64.2 + - - +
91H ARG* 3.2 7.4 + - - +
92H THR* 2.7 47.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
55H ARG* 2.9 41.4 + - - +
56H SER* 4.5 3.6 - - - +
57H VAL* 3.8 25.8 - - + +
60H LEU* 3.6 7.8 - - + +
85H GLU* 3.1 32.5 + - - +
86H THR 3.2 7.8 + - - +
88H LYS* 1.3 86.4 + - - +
90H VAL* 1.3 61.8 + - - +
92H THR* 3.5 3.0 + - - -
93H ALA* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ILE* 4.8 1.8 - - + -
60H LEU* 3.9 29.2 - - + -
64H ILE* 5.6 1.1 - - + -
68H MET* 5.0 2.9 - - + -
71H ALA* 4.2 20.4 - - + -
73H LEU* 5.6 3.4 - - + -
86H THR* 3.1 24.6 + - + +
87H ILE* 3.7 9.2 - - - +
89H ASN* 1.3 76.2 - - - +
91H ARG* 1.3 57.8 + - + +
93H ALA* 3.4 3.8 + - - +
94H THR* 2.8 42.4 + - - +
107H VAL* 4.1 19.3 - - + +
109H VAL* 4.8 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H ILE* 3.1 42.3 + - + +
88H LYS* 3.2 6.5 + - - +
90H VAL* 1.3 77.5 - - + +
92H THR* 1.3 57.7 + - - +
94H THR* 4.4 5.2 - - - -
95H GLU* 3.1 37.9 + - + +
109H VAL* 4.4 22.2 - - + +
234H GLN* 2.8 32.1 + - - +
235H ASP* 2.8 25.8 + - - +
236H VAL* 4.8 0.4 - - - +
237H ASP* 5.6 0.4 + - - -
460H ARG* 5.9 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H VAL* 4.1 21.0 - - + +
61H LYS* 5.8 0.9 - - - +
88H LYS* 2.7 37.9 + - - +
89H ASN* 3.8 5.7 - - - -
90H VAL 3.3 0.2 - - - -
91H ARG* 1.3 75.1 - - - +
93H ALA* 1.3 64.2 + - - +
95H GLU* 3.9 2.9 - - - +
96H SER* 3.2 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H VAL* 3.6 29.1 - - + +
60H LEU* 3.8 16.6 - - + -
61H LYS* 3.8 13.2 - - + +
64H ILE* 4.0 4.9 - - + -
89H ASN 3.1 15.5 + - - +
90H VAL 3.7 3.8 - - - +
92H THR* 1.3 79.4 - - - +
94H THR* 1.3 60.6 + - - +
96H SER* 2.6 23.1 + - - -
97H PHE* 3.4 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H ILE* 3.4 19.1 - - + +
90H VAL* 2.8 24.8 + - - +
91H ARG* 4.1 6.3 - - - -
93H ALA* 1.3 75.9 - - - +
95H GLU* 1.3 63.9 + - - +
96H SER 3.4 1.2 + - - -
97H PHE* 3.4 15.1 + - - +
104H TYR* 3.5 31.6 - - - +
105H ARG 3.7 18.2 - - - +
107H VAL* 3.5 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H ARG* 3.1 25.5 + - + +
92H THR* 3.9 4.3 - - - +
93H ALA 3.3 0.2 - - - -
94H THR* 1.3 77.5 - - - +
96H SER* 1.3 56.8 + - - +
97H PHE 3.1 5.6 - - - -
98H ALA* 3.1 37.6 + - + +
99H SER 4.7 0.7 + - - -
104H TYR* 2.6 30.1 + - - -
474H LYS* 5.3 4.2 + - - -
----------------------------------------------------------
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