Contacts of the helix formed by residues 110 - 127 (chain A) in PDB entry 4EUW
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 110 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PRO 3.6 4.1 + - - +
109A MET* 1.4 73.9 - - - +
111A ALA* 1.3 56.7 + - - +
112A PHE 3.4 1.7 + - - -
113A MET* 2.8 50.7 + - - +
114A VAL* 2.9 11.3 + - - +
158A ALA* 3.7 5.2 - - - -
6B T 2.8 17.5 + - - +
7B G 2.6 57.0 + - - +
8B A 4.3 19.5 - - - +
7C A 4.0 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASN* 1.3 73.7 - - - +
112A PHE* 1.3 61.7 + - - +
114A VAL* 4.5 0.4 - - - -
115A TRP 3.4 15.1 + - - -
143A TRP* 3.4 22.7 - - + -
154A PHE* 3.5 28.8 - - - +
155A VAL* 3.7 29.8 - - + -
158A ALA* 3.2 7.2 - - + +
7B G 4.9 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASN* 3.1 7.7 + - - +
111A ALA* 1.3 78.1 - - - +
113A MET* 1.3 65.0 + - + +
115A TRP* 3.4 11.3 + + - -
116A ALA* 2.8 48.5 + - + +
120A ARG* 6.0 0.2 - - - -
139A LEU* 3.6 40.2 - - + -
140A GLY* 3.9 5.2 - - - -
143A TRP* 3.6 27.1 - + + -
5B T 3.6 39.7 - - + -
6B T 3.1 52.9 - - - +
7B G 4.3 3.6 - - - -
8C A 5.4 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A MET* 3.5 27.0 - - + +
110A ASN* 2.8 34.5 + - - +
112A PHE* 1.3 77.8 - - + +
114A VAL* 1.3 63.2 + - - +
116A ALA* 4.0 4.8 - - - +
117A GLN* 3.5 16.3 + - - +
5B T 4.0 6.5 - - - +
6B T 3.6 16.2 - - + +
7C A 3.4 43.3 - - + +
8C A 3.5 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A MET* 3.6 36.1 - - + +
110A ASN 2.9 19.2 + - - +
111A ALA 3.9 5.4 - - - +
112A PHE 3.2 0.2 - - - -
113A MET* 1.3 76.1 - - - +
115A TRP* 1.3 64.2 + - - +
117A GLN* 3.5 14.7 + - - +
118A ALA* 4.3 3.5 + - - +
154A PHE* 4.1 18.9 - - + +
157A GLU* 3.8 24.0 - - + -
158A ALA* 4.3 11.2 - - - +
161A LEU* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA 3.4 4.0 + - - +
112A PHE* 3.6 19.3 - + - -
114A VAL* 1.3 78.4 - - - +
116A ALA* 1.3 86.9 + - - +
117A GLN 3.4 0.3 + - - -
118A ALA* 3.6 5.1 + - - +
119A ALA* 3.3 33.6 + - + +
139A LEU* 3.2 52.7 - - + -
142A LEU* 3.9 20.6 - - + -
143A TRP* 3.4 44.4 - + + -
146A LEU* 3.9 14.9 - - + +
154A PHE* 3.6 43.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 2.8 42.0 + - + +
113A MET* 4.2 7.4 - - - +
114A VAL 3.3 0.4 - - - -
115A TRP* 1.3 94.9 - - + +
117A GLN* 1.3 56.7 + - - +
119A ALA* 4.2 2.0 - - - -
120A ARG* 2.8 42.3 + - - +
139A LEU* 4.2 9.2 - - + -
8C A 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A MET* 3.4 28.4 - - - +
113A MET 3.5 15.2 + - - +
114A VAL 3.8 7.4 - - - +
115A TRP 3.2 1.2 - - - -
116A ALA* 1.3 79.5 - - - +
118A ALA* 1.3 59.4 + - - +
120A ARG* 4.0 5.8 - - - +
121A ARG* 3.5 38.3 + - - +
8C A 3.7 29.1 - - - +
9C A 4.1 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL 4.3 2.8 + - - +
115A TRP 3.6 6.2 + - - +
116A ALA 3.4 0.2 - - - -
117A GLN* 1.3 75.5 - - - +
119A ALA* 1.3 56.7 + - - +
121A ARG* 3.1 23.2 + - - +
122A LYS* 2.8 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A TRP* 3.3 38.9 + - + +
116A ALA 3.9 1.1 - - - +
118A ALA* 1.3 77.8 - - - +
120A ARG* 1.3 61.8 + - - +
122A LYS* 3.5 8.3 + - - +
123A LEU* 3.3 26.7 + - - +
139A LEU* 3.5 21.3 - - + -
142A LEU* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 6.0 0.4 - - - -
116A ALA* 2.8 32.5 + - - +
117A GLN* 4.0 5.8 - - - +
119A ALA* 1.3 73.5 - - - +
121A ARG* 1.3 60.1 + - + +
123A LEU* 3.2 8.7 + - - +
124A ALA* 2.8 27.9 + - + +
132A ASN* 3.0 42.9 + - - +
135A LEU* 4.1 10.9 - - + +
136A SER* 2.6 38.2 + - - +
139A LEU* 3.5 31.6 - - + +
5B T 4.8 0.4 + - - -
8C A 3.4 26.5 + - - -
9C A 3.5 39.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN* 3.5 39.6 + - - +
118A ALA* 3.1 22.5 + - - +
120A ARG* 1.3 79.8 - - + +
122A LYS* 1.3 59.9 + - - +
124A ALA* 4.1 9.2 - - + -
125A ASP* 3.0 57.1 + - - +
9C A 5.9 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA 2.8 20.3 + - - +
119A ALA* 3.6 10.3 - - - +
120A ARG 3.3 0.2 - - - -
121A ARG* 1.3 73.7 - - - +
123A LEU* 1.3 60.8 + - + +
125A ASP* 3.8 9.4 + - - +
126A GLN* 3.5 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ALA 3.3 12.5 + - - +
120A ARG* 3.2 8.3 + - - +
122A LYS* 1.3 78.0 - - + +
124A ALA* 1.3 60.6 + - - +
126A GLN* 3.0 14.2 + - - +
127A TYR* 2.9 51.5 + - + +
130A LEU* 6.1 0.9 - - + -
135A LEU* 4.6 21.3 - - + +
138A THR* 4.3 24.2 - - + -
139A LEU* 4.4 16.6 - - + -
142A LEU* 5.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 2.8 22.4 + - + +
121A ARG* 3.9 11.9 - - + +
123A LEU* 1.3 73.6 - - - +
125A ASP* 1.3 61.3 - - - +
127A TYR 3.3 10.0 - - - +
128A PRO* 3.1 29.7 - - + +
132A ASN* 5.4 2.0 - - - +
135A LEU* 4.1 16.9 - - + +
10C G 6.3 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.0 45.8 + - - +
122A LYS* 4.0 8.1 + - - +
123A LEU 3.2 0.4 - - - -
124A ALA* 1.3 77.4 - - - +
126A GLN* 1.3 61.5 + - + +
128A PRO* 4.4 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LYS 3.5 19.9 + - - +
123A LEU* 3.0 12.1 + - - +
125A ASP* 1.3 78.1 - - + +
127A TYR* 1.3 100.2 + - + +
128A PRO* 3.2 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 2.9 38.2 + - + +
124A ALA* 3.1 15.6 - - - +
126A GLN* 1.3 110.5 + - + +
128A PRO* 1.3 63.5 - - - +
129A HIS* 3.2 5.3 + - - +
130A LEU* 3.5 49.6 + - + +
135A LEU* 5.4 0.2 - - - +
----------------------------------------------------------
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