Contacts of the helix formed by residues 77 - 91 (chain F) in PDB entry 6G2T
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 ASN 77 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F ARG* 5.4 2.8 - - - +
67F LYS* 4.6 10.8 - - - +
69F PRO* 3.9 7.6 + - + +
75F VAL* 4.9 3.8 - - - +
76F THR* 1.3 87.4 + - - +
78F TRP* 1.3 66.8 + - - +
79F ASP* 2.7 35.9 + - - +
80F ASP* 3.4 25.7 + - + +
81F MET* 3.6 15.9 + - - +
204L GLY* 5.6 5.4 - - - -
205L GLN* 5.7 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F VAL* 3.2 45.8 + - + -
76F THR 5.4 1.6 - - - -
77F ASN* 1.3 76.2 + - - +
79F ASP* 1.3 66.0 + - - +
81F MET* 3.1 11.2 + - + +
82F GLU* 3.1 20.1 + - - +
85F TRP* 4.8 7.0 - + - -
113F ALA* 4.3 1.6 - - + -
114F ASN* 3.5 33.4 - - - -
117F LYS* 3.3 42.3 - - + +
118F MET* 3.9 14.8 - - + -
121F ILE* 3.2 36.3 - - + +
203L VAL 5.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F ARG* 5.0 5.0 + - - -
77F ASN* 2.7 36.6 + - - +
78F TRP* 1.3 78.5 - - - +
80F ASP* 1.3 83.2 + - - +
82F GLU* 3.2 13.8 + - - +
83F LYS* 3.1 36.3 + - - +
205L GLN* 4.3 21.8 - - + +
206L HIS* 5.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F VAL* 3.6 32.1 - - + +
36F ARG* 3.5 23.3 + - - -
67F LYS* 4.0 19.6 - - - +
69F PRO* 4.3 10.4 - - + +
77F ASN* 3.4 27.1 + - - +
78F TRP 3.3 0.6 - - - -
79F ASP* 1.3 94.6 + - - +
81F MET* 1.3 62.6 + - - +
83F LYS* 3.2 12.7 + - - +
84F ILE* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ASN* 4.2 13.2 - - - +
32F SER* 6.0 0.4 - - - -
69F PRO* 3.8 16.9 - - + +
70F ILE* 3.5 39.0 - - + -
75F VAL* 3.7 15.0 - - + -
77F ASN 3.6 8.9 + - - +
78F TRP* 3.1 16.2 + - + +
80F ASP* 1.3 80.0 - - - +
82F GLU* 1.3 55.9 + - - +
84F ILE* 3.2 11.9 + - + +
85F TRP* 2.9 76.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F TRP 3.1 12.5 + - - +
79F ASP* 3.2 16.3 + - - +
81F MET* 1.3 77.2 - - - +
83F LYS* 1.3 66.6 + - - +
85F TRP* 3.3 12.1 + - - +
86F HIS* 2.8 41.9 + - - +
121F ILE* 4.9 7.9 - - + -
125F THR* 3.6 33.7 - - + +
126F PHE* 3.9 10.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F VAL* 5.1 2.7 - - + -
36F ARG* 3.8 30.1 - - - +
50F ASP* 4.0 9.3 + - - +
51F SER* 4.1 11.8 - - - +
53F VAL* 4.0 23.1 - - + +
79F ASP* 3.1 27.2 + - - +
80F ASP* 3.2 17.2 + - - +
82F GLU* 1.3 85.6 - - - +
84F ILE* 1.3 57.2 + - - +
86F HIS* 3.4 8.6 + - - +
87F HIS* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F CYS* 3.4 29.8 - - - -
30F PHE* 4.0 17.0 - - + -
32F SER* 4.4 5.2 - - - -
33F ILE 4.3 11.7 - - - +
34F VAL* 4.0 12.1 - - + -
53F VAL* 3.6 21.5 - - + -
69F PRO* 3.4 34.5 - - + -
80F ASP 3.1 15.7 + - - +
81F MET* 3.2 14.1 + - + +
83F LYS* 1.3 73.7 - - - +
85F TRP* 1.3 61.4 + - + +
87F HIS* 3.2 2.8 + - - +
88F THR* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 4.3 17.1 - - + +
11F ASN* 2.8 30.8 - - + +
75F VAL* 6.4 0.2 - - + -
78F TRP* 4.8 4.0 - + - -
81F MET* 2.9 50.7 + - + +
82F GLU* 3.7 5.6 - - - +
84F ILE* 1.3 77.4 - - + +
86F HIS* 1.3 61.9 + - - +
88F THR* 2.8 23.2 + - + -
89F PHE* 2.8 21.4 + - + -
104F LEU* 4.4 7.2 - - + +
118F MET* 3.7 39.3 - - + -
121F ILE* 3.6 38.8 - - + -
122F MET* 3.3 28.7 - - + +
126F PHE* 3.9 12.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F GLU* 2.8 27.2 + - - +
83F LYS* 3.4 9.7 + - - +
85F TRP* 1.3 76.6 - - - +
87F HIS* 1.3 66.4 + - - +
90F TYR* 3.0 67.8 + + + +
91F ASN* 5.0 4.6 + - - -
126F PHE* 3.7 17.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F PHE* 3.5 25.0 - + - -
53F VAL* 3.1 41.7 + - + -
54F GLY* 4.4 2.7 - - - -
55F ASP* 4.7 6.5 + - - -
56F GLU* 4.8 9.6 + - - +
83F LYS 2.9 18.0 + - - +
84F ILE 3.2 5.4 + - - +
86F HIS* 1.3 78.5 + - - +
88F THR* 1.3 51.4 + - - +
91F ASN* 3.0 53.9 + - - +
92F GLU* 2.7 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 4.4 10.1 - - + +
16F CYS* 4.7 7.4 - - + -
18F ALA* 5.1 12.3 - - + -
30F PHE* 3.2 29.8 - - + -
84F ILE* 2.9 28.4 + - + +
85F TRP* 2.8 21.8 + - + -
87F HIS* 1.3 75.9 - - - +
89F PHE* 1.3 67.6 + - - +
92F GLU* 3.5 9.5 + - - +
93F LEU* 3.1 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F LEU* 3.6 31.4 - - + -
9F ILE* 3.4 33.0 - - + -
85F TRP* 2.8 37.3 + - + +
88F THR* 1.3 84.1 + - - +
90F TYR* 1.3 68.4 + - + +
93F LEU* 3.6 8.8 - - + +
94F ARG 2.7 26.3 + - - -
95F VAL* 3.0 24.4 + - + +
97F PRO* 3.8 32.3 - - + -
102F VAL* 4.1 14.6 - - + -
122F MET* 4.4 14.1 - - + -
126F PHE* 4.7 10.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F HIS* 3.0 60.8 + + + +
89F PHE* 1.3 86.3 - - + +
91F ASN* 1.3 69.0 + - - +
92F GLU 3.5 0.4 - - - -
94F ARG* 3.3 24.3 + - - +
95F VAL 4.9 7.4 - - - -
96F ALA* 5.9 1.8 - - + -
97F PRO* 4.6 14.5 - - + +
98F GLU* 5.4 2.8 + - - -
126F PHE* 4.2 21.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F HIS* 4.7 5.2 + - - +
87F HIS* 3.0 54.3 + - + +
90F TYR* 1.3 77.5 - - - +
92F GLU* 1.3 70.7 + - - +
94F ARG* 4.0 14.6 + - - -
----------------------------------------------------------
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