Contacts of the helix formed by residues 104 - 117 (chain E) in PDB entry 5ZR1
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 GLU 104 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ILE 5.7 0.2 - - - +
138D SER* 5.5 1.6 - - - -
141D THR* 3.3 31.7 + - + +
70E TRP* 5.9 1.3 - - - -
74E LEU* 3.3 14.7 - - - +
102E VAL* 3.7 1.2 - - - +
103E GLU* 1.3 91.4 + - + +
105E PRO* 1.3 78.9 - - + +
106E PHE 3.8 3.4 - - - +
107E LEU* 3.7 34.2 - - + +
108E LEU* 3.4 15.1 + - - +
13G G 5.4 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ILE* 3.9 31.6 - - + +
70E TRP* 4.4 13.2 - - + -
74E LEU* 4.0 23.8 - - + -
104E GLU* 1.3 92.2 - - + +
106E PHE* 1.3 59.2 + - - +
108E LEU* 3.8 5.1 - - - +
109E VAL* 3.4 21.8 + - - +
148E LYS* 3.7 33.9 - - + -
152E LEU* 4.5 5.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ILE* 3.9 11.6 + - + +
137D HIS* 3.4 31.4 - + + +
141D THR* 3.7 30.7 - - + -
144D ASN* 3.9 12.6 - - + -
145D GLY* 3.6 26.9 - - - -
148D THR* 4.1 20.6 - - + -
149D GLN* 4.6 13.0 - - + -
104E GLU* 3.2 1.8 - - - +
105E PRO* 1.3 76.4 - - - +
107E LEU* 1.3 70.9 + - + +
108E LEU 3.1 1.8 - - - -
109E VAL* 2.9 20.4 + - + +
110E LYS* 2.8 44.4 + - + -
155E LEU* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASN* 3.3 37.5 - - + +
141D THR* 6.0 0.2 - - + -
144D ASN* 6.3 2.2 - - + -
101E GLN 3.9 1.3 - - - +
102E VAL* 3.3 13.9 - - + +
103E GLU* 3.8 9.4 - - + +
104E GLU* 3.5 34.5 + - + +
105E PRO 3.5 0.4 - - - -
106E PHE* 1.3 84.4 - - + +
108E LEU* 1.3 57.4 - - - +
110E LYS* 3.7 30.7 - - - +
111E THR* 2.8 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E LEU* 3.6 46.9 - - + +
77E ILE* 4.0 32.1 - - + -
78E ALA* 4.0 17.3 - - + -
102E VAL* 4.1 6.0 - - + +
104E GLU 3.4 11.0 + - - +
105E PRO 3.8 10.1 - - - +
106E PHE 3.1 0.6 - - - -
107E LEU* 1.3 78.5 - - - +
109E VAL* 1.3 53.5 + - + +
111E THR* 3.2 1.6 + - - -
112E LEU* 2.8 53.9 + - + +
149E TYR* 5.0 0.2 - - + -
152E LEU* 4.2 24.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
136D ILE* 3.9 12.3 - - + -
149D GLN* 6.2 0.9 - - - +
105E PRO 3.4 16.6 - - - +
106E PHE* 2.9 21.5 + - + +
108E LEU* 1.3 75.6 - - + +
110E LYS* 1.3 58.2 + - - +
112E LEU* 3.8 1.1 - - + +
113E HIS* 2.9 29.4 + - + +
152E LEU* 3.7 24.7 - - + -
155E LEU* 3.7 33.0 - - + +
156E LEU* 3.8 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D THR* 3.7 34.5 - - + +
101E GLN* 6.1 1.2 - - - +
106E PHE* 2.8 29.0 + - + +
107E LEU* 3.7 29.1 - - - +
109E VAL* 1.3 78.5 - - - +
111E THR* 1.3 59.7 + - - +
113E HIS* 3.4 8.9 + - + +
114E ASN* 3.0 50.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ALA* 4.4 13.0 - - + -
82E GLN* 6.2 0.4 - - - -
97E TYR* 4.3 19.0 - - + -
98E ASP 5.4 4.1 + - - +
99E PRO* 5.9 0.4 - - + -
101E GLN* 6.0 0.7 - - - +
102E VAL* 3.3 20.0 - - + +
107E LEU* 2.8 24.1 + - - +
108E LEU* 3.7 3.4 - - - -
110E LYS* 1.3 77.9 + - - +
112E LEU* 1.3 60.8 + - + +
114E ASN* 3.1 9.7 + - - +
115E ILE* 2.8 46.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
77E ILE* 4.6 6.7 - - + +
78E ALA* 5.0 2.7 - - + -
81E VAL* 4.3 24.2 - - + -
108E LEU* 2.8 53.4 + - + +
109E VAL* 4.1 3.1 - - + +
111E THR* 1.3 72.8 - - - +
113E HIS* 1.3 59.9 + - - +
115E ILE* 4.4 11.9 - - + +
116E PHE* 3.1 55.5 + - + -
152E LEU* 5.5 4.9 - - + -
156E LEU* 4.2 25.6 - - + -
164E ILE* 4.5 14.8 - - + -
166E PHE* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D GLN* 3.3 40.2 + - - +
156D LYS* 5.9 5.2 - - - -
109E VAL* 2.9 22.0 + - + +
110E LYS* 3.6 9.2 - - + +
111E THR 3.2 0.2 - - - -
112E LEU* 1.3 77.9 - - - +
114E ASN* 1.3 68.9 + - - +
116E PHE* 4.5 1.5 - - - +
117E VAL* 3.3 43.0 + - + +
155E LEU 5.7 1.7 + - - +
156E LEU* 5.2 1.7 - - + +
157E PRO* 3.5 42.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D GLN* 5.5 0.2 - - - +
97E TYR* 3.6 45.2 + - + +
110E LYS* 3.0 46.2 + - - +
111E THR* 3.1 7.0 + - - +
113E HIS* 1.3 86.2 - - - +
115E ILE* 1.3 64.2 + - - +
117E VAL* 3.4 20.1 - - - +
118E GLN* 4.0 6.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ALA* 4.3 9.4 - - - +
81E VAL* 4.7 1.6 - - + -
82E GLN* 3.8 37.2 - - + +
85E LEU* 4.1 17.9 - - + -
97E TYR* 3.9 18.2 - - + -
111E THR* 2.8 36.7 + - + +
112E LEU* 4.1 16.2 - - + +
114E ASN* 1.3 76.1 - - - +
116E PHE* 1.3 76.5 + - + +
118E GLN* 3.3 18.1 - - - +
119E TYR* 3.2 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E VAL* 3.9 24.0 - - + -
85E LEU* 4.3 2.5 - - + -
112E LEU* 3.1 35.6 + - + +
113E HIS* 4.5 4.0 - - - +
114E ASN 3.3 0.4 - - - -
115E ILE* 1.3 87.6 - - + +
117E VAL* 1.3 63.7 + - + +
118E GLN 3.3 0.8 + - - -
119E TYR* 3.5 16.9 + - - +
120E GLU* 3.8 9.5 - - - +
128E LEU* 6.2 0.7 - - + -
156E LEU* 3.6 31.0 - - + -
157E PRO* 5.4 6.3 - - + -
160E SER* 3.7 21.0 + - - +
161E LYS* 5.2 0.7 + - - +
162E ILE* 3.7 51.1 + - + +
164E ILE* 4.3 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E TYR* 5.9 0.2 - - - +
113E HIS* 3.3 39.5 - - + +
114E ASN* 3.4 24.0 - - - +
116E PHE* 1.3 78.5 - - + +
118E GLN* 1.3 60.2 + - + +
119E TYR 3.3 0.2 - - - -
120E GLU* 3.3 30.4 - - - +
157E PRO* 5.5 4.0 - - + -
----------------------------------------------------------
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