Contacts of the helix formed by residues 103 - 118 (chain E) in PDB entry 4GOO
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 103 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E SER* 3.1 10.4 + - - +
102E GLN* 1.3 76.6 - - - +
104E PRO* 1.4 69.4 - - - +
105E PHE* 2.8 35.3 + - - +
106E ARG* 3.2 24.0 + - + +
107E ARG* 2.9 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E SER* 4.4 17.8 + - - +
65E ILE* 3.7 15.0 - - + +
102E GLN 3.1 12.7 - - - +
103E ASP* 1.4 84.1 - - - +
105E PHE* 1.3 62.4 + - - +
107E ARG* 3.6 9.8 + - + +
108E ALA* 3.2 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E ILE* 3.8 25.9 - - + +
69E ARG* 3.5 40.1 - - + +
72E GLU* 3.5 38.6 - - + -
73E TYR* 3.8 27.4 - + + -
76E ALA* 4.1 12.3 - - + -
103E ASP* 2.8 17.6 + - - +
104E PRO* 1.3 72.4 - - - +
106E ARG* 1.3 64.8 + - + +
108E ALA* 3.0 15.1 + - - +
109E VAL* 3.2 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E LEU* 4.0 14.8 - - - +
94E PHE* 4.3 14.5 - - - -
97E GLU* 2.7 39.6 + - + +
101E SER* 4.5 9.4 - - - +
103E ASP* 3.2 27.0 + - + +
105E PHE* 1.3 80.6 - - + +
107E ARG* 1.4 64.2 + - - +
109E VAL* 3.2 31.0 + - - +
110E LEU* 3.0 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E ASP* 2.7 38.0 + - - -
98E PHE* 3.0 61.5 + - + -
99E ASN* 4.5 5.3 + - - +
101E SER* 3.5 37.1 + - - -
102E GLN* 4.6 2.2 - - - +
103E ASP 2.9 28.8 + - - +
104E PRO* 3.9 8.2 - - + +
106E ARG* 1.4 72.7 - - - +
108E ALA* 1.3 52.5 + - - +
110E LEU* 3.4 1.9 + - - -
111E PHE* 2.7 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E SER* 5.7 0.4 - - - +
62E LEU* 4.0 27.3 - - + +
65E ILE* 4.1 17.7 - - + -
73E TYR* 3.0 30.3 + - + -
104E PRO 3.2 13.0 + - - +
105E PHE 3.0 11.0 + - - +
107E ARG* 1.3 74.9 - - - +
109E VAL* 1.3 64.4 + - - +
111E PHE* 3.6 7.8 - - - +
112E LEU 3.4 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E TYR* 3.8 20.2 - - + -
76E ALA* 4.3 19.1 - - + +
77E ALA* 4.3 10.0 - - - +
80E LEU* 3.8 27.5 - - + +
105E PHE* 3.5 34.5 - - + +
106E ARG* 3.3 26.7 - - - +
108E ALA* 1.3 71.5 - - - +
110E LEU* 1.3 71.3 + - - +
111E PHE 3.0 1.2 + - - -
112E LEU* 3.0 15.2 + - - +
113E TYR* 3.5 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E LEU* 4.1 14.4 - - + -
94E PHE* 3.6 52.5 - - + +
97E GLU* 4.0 17.5 - - + +
98E PHE* 4.1 26.9 - - + +
101E SER* 5.6 0.7 - - - -
106E ARG* 3.0 56.7 + - + +
107E ARG 4.0 2.7 - - - +
109E VAL* 1.3 71.6 - - - +
111E PHE* 1.3 65.2 + - - +
113E TYR* 2.9 5.5 + - + +
114E LEU* 2.9 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 4.2 13.7 - - + -
56E ASN* 5.1 1.6 - - - -
58E ASP* 3.7 32.3 - - + -
59E LEU* 4.6 19.1 - - + -
62E LEU* 3.6 32.8 - - + -
98E PHE* 4.1 17.1 - + + -
107E ARG 2.7 24.5 + - - +
108E ALA* 3.6 8.1 - - - +
109E VAL 3.0 0.2 + - - -
110E LEU* 1.3 71.8 - - - +
112E LEU* 1.3 52.9 + - - +
114E LEU* 3.2 11.2 + - + +
115E ASN* 2.7 38.5 + - + +
123E CYS* 4.0 22.4 - - + -
125E TYR* 4.0 9.9 - - - -
131E PHE* 4.9 9.9 - + - -
301E 0Y2 5.4 4.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E PHE* 4.0 26.9 - - + +
8E LEU* 4.1 15.9 - - + -
62E LEU* 5.4 1.8 - - + -
73E TYR* 3.2 26.9 - - + +
77E ALA* 4.4 5.6 - - + -
81E PHE* 4.2 9.0 - - + -
108E ALA 3.4 2.0 + - - +
109E VAL 3.0 6.9 + - - +
111E PHE* 1.3 78.2 - - + +
113E TYR* 1.3 69.9 + - - +
115E ASN* 3.0 5.3 + - - +
116E ARG* 2.8 34.0 + - + +
143E PHE* 4.2 16.8 - - + -
144E PRO* 4.2 8.3 - - + -
148E LEU* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E LEU* 3.9 31.0 - - + -
81E PHE* 4.0 15.3 - + + -
85E THR* 3.0 27.8 + - - -
90E VAL* 4.1 0.5 - - - +
91E TYR* 3.1 42.7 + + - +
94E PHE* 3.5 37.5 - + + -
109E VAL 3.5 2.8 + - - +
110E LEU* 2.9 11.0 + - + +
112E LEU* 1.3 76.9 - - - +
114E LEU* 1.4 61.5 + - + +
116E ARG* 2.7 23.2 + - - -
117E TYR* 2.7 65.9 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E TYR* 4.0 27.3 + - + +
94E PHE 4.6 0.7 - - - -
95E ARG* 3.8 33.4 - - + +
98E PHE* 3.8 37.9 - - + -
110E LEU* 2.9 25.0 + - + +
111E PHE* 3.5 8.1 - - + +
113E TYR* 1.4 83.1 - - + +
115E ASN* 1.3 62.3 + - - +
118E GLY* 3.1 23.0 + - - -
121E GLY* 5.2 0.3 - - - -
122E LEU 5.2 1.2 - - - +
131E PHE* 3.9 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 3.8 29.5 - - + +
9E LYS* 3.3 46.7 + - - +
111E PHE* 2.7 26.3 + - + +
112E LEU* 3.0 3.5 + - - +
114E LEU* 1.3 74.5 - - - +
116E ARG* 1.3 69.5 + - - +
118E GLY 4.3 0.2 + - - -
121E GLY* 3.5 32.7 + - - -
122E LEU 5.2 4.7 + - - +
123E CYS* 6.2 0.2 - - - +
131E PHE* 5.2 2.4 - - + -
301E 0Y2 4.5 11.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ALA 3.9 7.7 + - - -
7E PHE* 2.8 35.7 + - - +
8E LEU 4.0 0.2 - - - -
9E LYS* 3.3 55.0 + - - +
81E PHE* 3.6 38.4 - - + -
112E LEU* 2.8 16.2 + - + +
113E TYR 2.7 11.6 + - - +
115E ASN* 1.3 80.7 + - - +
117E TYR* 1.3 60.9 - - + +
118E GLY 3.4 1.6 - - - -
138E TYR* 4.2 5.4 - - - -
141E PRO* 4.2 10.5 - - + +
142E TYR* 3.5 42.5 + - - +
144E PRO* 4.2 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E LEU 4.2 0.4 - - - -
81E PHE* 3.5 31.2 - + - +
82E VAL 3.1 21.8 + - - -
85E THR* 3.4 22.0 + - - -
86E ASN* 3.6 25.1 - - + -
91E TYR* 3.7 9.2 - - + -
113E TYR* 2.7 65.5 + + + +
116E ARG* 1.3 75.4 - - + +
118E GLY* 1.3 56.0 + - - +
135E PHE* 3.4 13.4 - + + -
136E GLY* 3.0 21.4 + - - -
138E TYR* 4.5 5.1 - - - -
141E PRO* 3.5 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LYS* 4.3 0.9 + - - -
91E TYR* 3.9 9.6 - - - -
114E LEU 3.1 18.6 + - - -
115E ASN 4.3 0.2 + - - -
116E ARG 3.4 1.8 - - - -
117E TYR* 1.3 80.1 - - - +
119E TYR* 1.3 69.3 + - - -
120E ASN 3.1 1.4 + - - -
121E GLY* 2.9 16.3 + - - -
122E LEU 6.1 0.4 - - - -
133E VAL* 4.4 3.4 - - - -
134E PRO 3.8 8.1 - - - -
136E GLY* 3.8 3.4 - - - -
138E TYR* 3.4 9.7 - - - -
----------------------------------------------------------
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