Contacts of the helix formed by residues 111 - 128 (chain A) in PDB entry 3U8Z
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 GLN 111 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY 2.7 27.1 + - - -
56A LEU* 3.7 2.8 - - - -
57A ARG* 2.7 61.3 + - - +
58A GLU* 3.3 23.2 + - - +
109A LEU 4.1 0.7 - - - +
110A VAL* 1.4 78.8 - - + +
112A GLU* 1.3 62.9 + - - +
113A ILE* 4.3 6.8 - - + +
114A THR* 2.9 33.1 + - + +
115A GLN* 3.3 5.4 + - - +
200A ARG* 3.5 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLN* 1.3 68.7 - - - +
113A ILE* 1.4 55.5 + - - +
115A GLN* 3.3 12.9 + - - +
116A HIS* 2.7 38.9 + - + +
198A ARG* 2.7 43.4 + - - -
200A ARG* 3.2 34.5 - - + +
201A ASP* 2.8 27.9 + - - +
204A GLU* 4.8 3.8 - - - +
55C GLY* 3.9 10.2 - - - +
57C ARG* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.5 37.7 - - + +
55A GLY 4.2 4.7 - - - +
56A LEU* 3.9 27.4 - - + -
111A GLN* 4.3 6.7 - - + +
112A GLU* 1.4 75.9 - - - +
114A THR* 1.3 57.7 + - + +
116A HIS* 3.2 15.9 + - + +
117A LEU* 2.8 61.1 + - + +
53C THR 3.3 27.8 - - - +
55C GLY* 4.0 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.0 34.1 - - + -
58A GLU* 3.0 32.7 + - + +
61A PHE* 5.5 0.2 - - - -
62A PHE* 4.6 12.6 - - - -
109A LEU* 3.5 20.4 - - - +
111A GLN* 2.9 24.3 + - + +
112A GLU 3.3 0.2 - - - -
113A ILE* 1.3 70.2 - - - +
115A GLN* 1.3 67.8 + - - +
117A LEU* 3.4 1.1 + - - +
118A PHE* 3.0 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 4.0 13.0 - - + -
111A GLN 3.3 8.9 + - - +
112A GLU* 3.4 16.9 - - - +
114A THR* 1.3 81.6 + - - +
116A HIS* 1.3 54.7 + - - +
119A PHE* 2.9 30.5 + - - +
200A ARG* 3.5 27.0 + - - +
201A ASP 2.9 27.5 + - - +
202A GLU* 5.0 2.6 + - - -
204A GLU* 3.3 20.1 - - + +
205A MET* 3.4 48.6 - - + +
208A LEU* 3.6 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 2.7 38.4 + - - -
112A GLU* 2.7 23.5 + - + +
113A ILE* 3.4 13.7 - - + +
115A GLN* 1.3 73.4 - - - +
117A LEU* 1.3 62.1 + - - +
119A PHE* 3.3 4.3 + - - +
120A LEU* 3.1 44.8 + - + +
204A GLU* 2.6 38.1 + - - +
52C ARG* 3.4 47.4 + - + +
55C GLY* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 4.5 17.9 - - - -
29A MET* 4.2 13.2 - - + +
30A ASP* 3.8 21.5 - - - +
54A LEU* 4.4 9.6 - - + -
56A LEU* 4.6 5.8 - - + -
62A PHE* 4.0 23.6 - - + -
96A PHE* 3.8 31.9 - - + +
113A ILE* 2.8 43.1 + - + +
114A THR* 4.0 3.4 - - - +
116A HIS* 1.3 70.1 - - - +
118A PHE* 1.3 64.8 + - - +
120A LEU* 3.6 4.4 + - - +
121A GLN* 3.2 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 3.7 21.5 - + + -
62A PHE* 3.7 18.2 - + - -
98A ALA* 3.5 21.3 - - + -
100A PHE 3.2 26.5 - - - -
101A TYR* 3.7 22.9 - + - -
102A PRO* 3.6 22.4 - - + -
109A LEU* 3.7 34.3 - - + -
114A THR 3.0 24.7 + - - +
115A GLN 4.0 1.1 - - - +
117A LEU* 1.3 73.2 - - - +
119A PHE* 1.3 65.0 + - - +
121A GLN* 3.3 4.7 + - + -
122A VAL* 2.9 31.8 + - + +
208A LEU* 3.9 9.0 - - + -
217A TYR* 4.8 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLN 2.9 20.3 + - - +
116A HIS* 3.3 3.3 + + - +
118A PHE* 1.3 75.2 - - - +
120A LEU* 1.3 71.4 + - + +
122A VAL* 4.0 0.7 - - - +
123A LYS* 2.9 62.9 + - + +
145A ALA* 4.1 7.2 - - - -
148A ALA* 3.7 24.0 - - + -
203A ALA 5.1 0.2 - - - -
204A GLU* 3.3 44.9 - - + +
207A TYR* 3.4 50.2 - + + -
208A LEU* 3.8 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 3.4 39.1 - - + +
30A ASP* 3.5 35.7 - - - +
116A HIS* 3.1 36.1 + - + +
117A LEU* 4.1 2.2 - - - +
119A PHE* 1.3 93.2 - - + +
121A GLN* 1.3 64.7 + - - +
123A LYS* 3.9 17.6 + - - +
124A LYS* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 3.9 14.9 - - + +
62A PHE* 5.3 1.2 - - - -
97A LEU* 3.5 26.7 - - + +
98A ALA* 2.8 51.1 + - - +
101A TYR* 3.1 23.9 + - - +
117A LEU 3.2 16.4 + - - +
118A PHE* 3.8 5.8 - - + +
120A LEU* 1.3 78.6 - - - +
122A VAL* 1.4 61.4 + - + +
124A LYS* 3.5 5.0 + - - +
125A GLN* 3.3 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 4.0 20.9 - - + -
118A PHE* 2.9 23.5 + - + +
119A PHE 4.1 0.9 - - - +
121A GLN* 1.4 72.3 - - + +
123A LYS* 1.3 58.5 + - - +
125A GLN* 3.1 12.7 + - - +
126A ILE* 3.0 30.9 + - + +
131A ILE* 4.2 7.4 - - + -
207A TYR* 4.3 4.3 - - + -
208A LEU* 3.9 13.0 - - + -
211A ALA* 3.6 30.3 - - + -
217A TYR* 3.6 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 2.9 54.4 + - + +
120A LEU* 3.9 17.8 + - - +
122A VAL* 1.3 76.2 - - - +
124A LYS* 1.4 56.3 + - - +
126A ILE* 3.1 2.6 + - - +
127A LEU* 2.9 53.2 + - + +
145A ALA* 3.9 20.2 - - + -
207A TYR* 3.3 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 3.9 20.9 - - + -
120A LEU 3.1 17.2 + - - +
121A GLN 3.7 6.1 - - - +
122A VAL 3.3 0.2 - - - -
123A LYS* 1.4 76.5 - - - +
125A GLN* 1.3 57.4 + - + +
127A LEU* 3.4 6.8 + - + +
128A ASP* 2.8 69.8 + - - +
130A LYS* 5.0 6.4 - - - +
70B ASP* 6.0 2.2 - - - -
289B LYS* 3.8 16.6 - - - +
291B ARG* 4.8 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 3.0 32.0 + - - -
121A GLN* 3.3 29.1 + - - +
122A VAL* 3.1 11.8 + - - +
124A LYS* 1.3 75.8 - - + +
126A ILE* 1.3 62.1 + - - +
128A ASP* 4.5 2.0 - - - -
129A GLU 3.2 1.6 + - - -
130A LYS* 2.9 52.3 + - + +
131A ILE* 3.2 36.1 + - + +
218A GLY 5.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 3.0 23.6 + - + +
123A LYS 3.1 6.5 + - - +
125A GLN* 1.3 76.1 - - - +
127A LEU* 1.3 72.8 + - + +
129A GLU* 3.2 14.0 + - - +
131A ILE* 3.9 22.3 - - + +
133A CYS* 4.5 14.6 - - + -
138A SER* 5.5 3.8 - - - +
141A LEU* 3.9 21.1 - - + -
207A TYR* 3.5 22.7 - - + +
211A ALA* 4.8 3.8 - - + -
214A LEU* 3.6 31.4 - - + -
225B ARG* 3.9 14.7 + - - +
231B GLU* 4.2 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LYS* 2.9 47.3 + - + +
124A LYS* 4.0 5.2 - - - +
126A ILE* 1.3 84.9 - - + +
128A ASP* 1.4 61.6 + - - +
129A GLU* 4.1 1.6 - - - +
142A ALA* 6.5 1.8 - - + -
207A TYR* 5.3 1.1 - - - +
225B ARG* 2.6 31.5 + - - +
288B SER* 3.7 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 2.8 52.9 + - - +
125A GLN 4.2 1.6 - - - +
127A LEU* 1.4 75.4 - - - +
129A GLU* 1.3 68.4 + - - +
130A LYS* 3.5 37.7 + - + +
223B ALA* 3.7 13.9 - - - +
288B SER* 4.6 7.5 + - - -
289B LYS* 3.4 27.0 + - - +
----------------------------------------------------------
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