Contacts of the helix formed by residues 101 - 119 (chain E) in PDB entry 3UNF
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 PRO 101 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ARG* 4.0 16.8 - - - +
99E PRO 3.4 9.4 - - - +
100E LEU* 1.3 96.4 - - + +
102E VAL* 1.3 66.3 + - - +
103E SER* 3.3 5.4 - - - +
104E ARG* 3.2 44.9 + - + +
105E LEU* 3.3 9.0 + - - +
135E ASP* 3.7 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E HIS* 4.8 1.1 - - + -
67E ILE* 3.9 22.9 - - + -
100E LEU 3.4 0.2 + - - -
101E PRO* 1.3 70.1 - - - +
103E SER* 1.3 63.8 + - - +
105E LEU* 3.2 4.6 + - + +
106E VAL* 3.1 33.0 + - + +
131E ILE* 4.4 16.4 - - + +
133E GLY* 3.9 28.3 - - - +
134E TYR 4.2 2.2 - - - +
135E ASP* 3.0 20.5 + - + +
140E HIS* 4.0 18.4 - - + -
142E PHE* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E PRO* 3.3 3.8 - - - +
102E VAL* 1.3 77.7 + - - +
104E ARG* 1.3 61.7 + - - +
106E VAL* 3.6 3.7 + - - +
107E SER* 3.1 29.3 + - - -
135E ASP* 5.0 2.4 + - - -
137E MET* 6.0 1.0 - - - +
140E HIS* 4.9 10.9 + - - -
142E PHE* 4.2 24.1 - - - -
150E TYR* 5.2 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ARG* 4.4 17.8 - - - +
100E LEU* 4.1 13.0 - - + -
101E PRO* 3.2 36.0 + - + +
103E SER* 1.3 77.5 - - - +
105E LEU* 1.3 66.2 + - - +
107E SER* 3.3 9.5 + - - -
108E LEU* 3.1 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E VAL* 4.5 1.3 - - + -
67E ILE* 3.4 32.3 - - + -
84E PHE* 5.5 0.7 - - + -
85E MET* 3.7 57.4 - - + +
88E GLU* 4.0 21.5 - - + -
89E CYS* 3.9 10.8 - - - -
100E LEU* 3.8 18.3 - - + +
101E PRO 3.3 6.6 + - - +
102E VAL* 3.2 9.1 + - + +
104E ARG* 1.3 77.7 - - - +
106E VAL* 1.3 64.9 + - + +
108E LEU* 3.2 8.6 + - + +
109E ILE* 3.2 24.5 + - + +
131E ILE* 5.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E VAL* 3.1 21.5 + - + +
103E SER 3.8 4.3 - - - +
105E LEU* 1.3 76.4 - - + +
107E SER* 1.3 57.6 + - - +
109E ILE* 3.2 9.8 + - + +
110E GLY* 2.9 25.8 + - - -
131E ILE* 4.0 13.5 - - + -
142E PHE* 3.7 40.4 - - + -
144E THR* 4.1 14.4 - - + -
150E TYR* 3.6 37.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E SER 3.1 17.2 + - - -
104E ARG* 3.4 13.0 - - - -
105E LEU 3.3 0.4 - - - -
106E VAL* 1.3 76.1 - - - +
108E LEU* 1.3 58.1 + - - +
110E GLY* 3.4 1.4 + - - -
111E SER* 3.0 29.5 + - - -
150E TYR* 3.0 29.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
84E PHE* 3.9 16.9 - - + -
88E GLU* 3.4 38.8 - - + +
100E LEU* 4.4 11.2 - - + -
104E ARG* 3.1 20.5 + - + +
105E LEU* 3.2 13.0 + - - +
107E SER* 1.3 76.5 - - - +
109E ILE* 1.3 59.3 + - - +
111E SER* 3.4 7.1 + - - -
112E LYS* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LEU* 3.7 19.7 - - + -
84E PHE* 4.2 12.3 - - + -
85E MET* 3.8 46.0 - - + -
105E LEU* 3.2 16.9 + - + +
106E VAL* 3.2 15.5 + - - +
108E LEU* 1.3 76.0 - - - +
110E GLY* 1.3 54.0 + - - +
112E LYS* 4.4 1.3 - - - +
113E THR* 2.7 53.3 + - - +
129E LEU* 5.1 1.8 - - + -
131E ILE* 3.9 13.2 - - + -
144E THR* 4.2 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E VAL 2.9 14.3 + - - -
107E SER 3.4 4.9 + - - -
108E LEU 3.3 0.2 - - - -
109E ILE* 1.3 76.9 - - - +
111E SER* 1.3 58.4 + - - +
114E GLN* 3.4 6.6 + - - +
144E THR* 6.0 0.2 - - - +
148E ALA* 3.3 43.4 - - - +
150E TYR* 3.8 13.7 - - - -
82F ALA* 5.0 2.8 - - - +
85F ARG* 6.0 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E SER 3.0 16.8 + - - -
108E LEU* 3.8 9.6 - - - -
110E GLY* 1.3 76.3 - - - +
112E LYS* 1.3 62.5 + - - +
114E GLN* 3.6 14.2 + - - +
115E ILE* 3.6 18.0 - - - +
85F ARG* 5.5 2.3 - - - +
86F SER* 5.2 6.4 + - - -
89F ASP* 2.9 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LEU* 5.6 3.4 - - + -
84E PHE* 3.5 50.1 - - + -
108E LEU 2.8 21.8 + - - +
109E ILE* 3.9 2.2 - - + +
111E SER* 1.3 70.8 - - - +
113E THR* 1.3 61.4 + - - +
114E GLN 3.1 1.6 - - - -
115E ILE* 3.4 19.8 + - + +
116E PRO* 3.1 23.4 - - - +
122E ARG* 5.8 4.0 - - - +
125E TYR* 3.8 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E LEU* 4.4 9.5 - - + +
109E ILE* 2.7 44.0 + - - +
112E LYS* 1.3 72.4 - - - +
114E GLN* 1.3 59.1 + - - +
116E PRO* 3.3 9.6 - - - +
117E THR* 3.5 14.2 - - - +
124E PRO* 5.6 0.2 - - - +
125E TYR* 3.9 31.6 + - + +
145E CYS 3.9 13.9 - - - +
146E PRO 3.5 22.7 - - - +
148E ALA* 3.8 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E GLY 3.4 16.8 + - - +
111E SER* 3.7 8.3 - - - +
112E LYS 3.1 0.4 - - - -
113E THR* 1.3 77.9 - - - +
115E ILE* 1.3 72.4 + - - +
117E THR* 2.6 30.1 + - - +
118E GLN* 2.8 31.6 + - - +
148E ALA* 3.5 12.3 - - + +
82F ALA* 3.3 27.6 - - + +
83F ASP* 2.9 23.1 + - - +
86F SER* 3.7 23.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
111E SER 3.6 17.9 - - - +
112E LYS* 3.7 20.2 - - + +
114E GLN* 1.3 83.1 + - - +
116E PRO* 1.4 67.5 - - + +
118E GLN* 3.2 14.9 + - - +
119E ARG* 3.5 49.3 + - - +
122E ARG* 4.0 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E VAL* 3.6 11.6 - - - +
112E LYS* 3.1 14.4 - - + +
113E THR 3.3 13.0 - - - +
115E ILE* 1.4 91.1 - - + +
117E THR* 1.3 58.6 + - - +
118E GLN 3.2 1.1 + - - -
119E ARG 3.7 1.4 - - - +
122E ARG* 3.4 58.7 - - + +
123E ARG 3.1 26.3 + - - +
124E PRO* 4.9 0.9 - - + -
125E TYR* 3.6 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E VAL* 3.4 35.2 - - - +
16E ILE* 5.2 4.2 - - - +
19E ILE* 4.1 32.5 - - + +
113E THR 3.5 18.6 - - - +
114E GLN* 2.6 30.0 + - - +
116E PRO* 1.3 78.6 - - - +
118E GLN* 1.3 56.8 + - - +
124E PRO* 4.3 17.3 - - + -
146E PRO 4.3 7.4 - - - +
148E ALA* 5.1 4.7 - - - +
83F ASP* 4.9 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E THR* 3.3 17.7 - - - +
114E GLN* 2.8 33.4 + - - +
115E ILE 3.2 8.6 + - - +
116E PRO 3.2 0.6 - - - -
117E THR* 1.3 80.2 + - - +
119E ARG* 1.3 62.4 + - + +
83F ASP* 4.8 11.2 + - - +
86F SER* 4.9 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 6.0 6.5 - - - +
119D ASP* 3.2 26.5 + - - +
7E VAL* 3.6 12.8 - - - +
8E THR* 3.6 2.9 - - - -
115E ILE* 3.5 44.0 + - - +
116E PRO 3.8 0.6 + - - -
118E GLN* 1.3 84.4 - - + +
120E TYR* 1.3 64.6 + - - +
122E ARG* 3.3 37.4 + - + +
----------------------------------------------------------
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