Contacts of the helix formed by residues 97 - 109 (chain F) in PDB entry 2GVG
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 97 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F VAL* 4.8 2.7 + - - +
23F TYR* 3.6 50.1 - - + +
95F VAL 3.4 2.2 + - - -
96F PHE* 1.3 76.5 - - - +
98F GLU* 1.3 61.5 + - - +
99F LYS* 3.7 8.3 - - - +
100F GLY* 2.9 30.2 - - - +
101F TRP* 3.3 25.0 + - + -
143F TRP* 4.0 19.0 + - + -
147F TRP* 5.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F LYS* 4.8 6.1 + - - -
80F ILE* 3.9 15.3 - - + +
81F GLN* 4.3 8.3 + - - -
84F LYS* 3.0 40.7 + - + +
96F PHE* 3.0 31.6 + - + +
97F ASN* 1.3 71.6 - - - +
99F LYS* 1.3 61.0 + - + +
101F TRP* 3.3 2.9 + - - +
102F ASN* 2.9 50.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ASN* 3.3 7.0 - - - +
98F GLU* 1.3 80.2 - - + +
100F GLY* 1.3 56.8 + - - +
102F ASN* 3.1 8.0 + - - +
103F TYR* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ASN* 2.9 30.0 - - - +
99F LYS* 1.3 75.1 - - - +
101F TRP* 1.3 60.5 + - - +
103F TYR* 3.5 18.5 - - - +
104F ILE* 3.6 8.0 + - - +
141F CYS* 5.3 0.3 - - - -
143F TRP* 3.4 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ILE* 4.1 16.8 - - + -
12F LEU* 3.7 19.0 - - + +
75F VAL* 3.4 37.8 - - + +
80F ILE* 3.8 23.3 - - + +
96F PHE* 3.5 25.8 - + + -
97F ASN* 3.3 15.7 + - + +
98F GLU 4.0 5.4 - - - +
99F LYS 3.2 0.4 - - - -
100F GLY* 1.3 75.4 - - - +
102F ASN* 1.3 66.1 + - - +
103F TYR 3.1 0.4 - - - -
104F ILE* 3.3 23.1 + - + +
105F LEU* 3.1 17.5 + - - +
112F LEU* 4.0 8.5 - - + -
143F TRP* 3.3 27.8 - + - -
144F LEU* 4.2 16.6 - - + -
147F TRP* 3.5 46.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F LYS* 4.1 20.7 - - - +
80F ILE* 3.9 19.8 - - - +
98F GLU* 2.9 43.8 + - - +
99F LYS* 3.5 7.7 - - - +
101F TRP* 1.3 74.2 - - - +
103F TYR* 1.3 60.6 + - - +
105F LEU* 3.2 6.7 + - - +
106F GLU* 2.8 53.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F LYS 2.9 12.1 + - - +
100F GLY* 3.5 13.5 - - - +
101F TRP 3.1 0.2 - - - -
102F ASN* 1.3 78.6 - - - +
104F ILE* 1.3 59.4 + - + +
106F GLU* 4.8 4.7 - - - -
107F LYS* 2.9 67.4 + - + +
108F TYR* 4.3 3.4 - + - -
138F ASP* 2.6 33.6 + - - -
140F GLU* 3.7 36.3 - - + +
141F CYS* 3.9 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F VAL* 4.2 9.2 - - + -
100F GLY 3.6 5.3 + - - +
101F TRP* 3.3 19.9 + - + +
102F ASN 3.2 0.4 - - - -
103F TYR* 1.3 77.2 - - - +
105F LEU* 1.3 60.4 + - - +
108F TYR* 3.0 28.2 + - + -
110F GLY* 3.1 20.9 + - - +
111F HIS 3.9 20.9 - - - +
112F LEU* 4.6 2.0 - - + +
113F PRO* 4.1 7.2 - - + -
141F CYS* 3.8 20.9 - - - -
143F TRP* 3.9 27.1 - - + -
144F LEU* 4.0 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F LYS* 3.7 22.0 - - - +
75F VAL* 3.5 29.6 - - + +
76F THR* 4.0 4.7 - - - -
77F LYS* 3.8 36.8 - - + +
80F ILE* 4.2 9.4 - - + -
101F TRP 3.1 13.8 + - - +
102F ASN* 3.7 11.4 - - - +
104F ILE* 1.3 78.6 - - - +
106F GLU* 1.3 63.0 + - + +
109F ASP* 2.8 30.7 + - - +
110F GLY* 3.4 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ASN* 2.8 44.2 + - + +
103F TYR* 4.3 4.0 - - - +
105F LEU* 1.3 79.8 - - + +
107F LYS* 1.3 61.1 + - + +
109F ASP 4.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F TYR* 2.9 50.8 + - + +
106F GLU* 1.3 80.0 - - - +
108F TYR* 1.3 97.9 + - + +
109F ASP 3.7 0.2 - - - -
138F ASP* 4.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F TYR* 4.3 5.6 - + - -
104F ILE* 3.0 15.8 + - - +
107F LYS* 1.3 113.9 - - + +
109F ASP* 1.3 72.2 + - - +
110F GLY 3.1 0.9 - - - -
111F HIS* 3.0 43.8 + - + +
113F PRO* 3.9 28.3 - - + -
137F THR* 5.5 0.4 + - - -
138F ASP* 2.7 33.6 + - + +
464F ASN* 6.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F LYS* 3.0 44.5 + - - +
105F LEU* 2.8 21.3 + - - +
106F GLU 4.4 1.6 + - - -
107F LYS 3.7 1.4 - - - -
108F TYR* 1.3 79.8 - - - +
110F GLY* 1.3 57.0 + - - +
111F HIS* 3.3 17.2 + - + +
----------------------------------------------------------
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