Contacts of the helix formed by residues 107 - 118 (chain B) in PDB entry 4ZCU
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 107 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 3.9 4.6 + - - +
103B ASP* 2.7 22.5 - - - +
105B LYS* 3.1 28.2 + - - +
106B ILE* 1.3 80.5 - - - +
108B ALA* 1.3 65.8 + - - +
109B SER* 3.2 5.6 - - - +
110B GLU* 2.9 28.4 + - + +
111B ILE* 3.4 5.0 + - - +
131B LEU* 3.6 3.6 - - - -
140B MET 5.2 1.8 - - - -
141B THR* 5.3 2.5 - - + -
1003B CA 2.4 27.4 - - - -
1007B SO4 3.3 33.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 1.3 74.3 - - - +
109B SER* 1.3 56.3 + - - +
111B ILE* 3.0 3.5 + - - +
112B VAL* 2.9 29.9 + - - +
124B GLU* 3.0 38.4 - - - +
127B ALA* 3.3 13.5 - - + +
128B GLU* 3.7 19.1 - - + +
131B LEU* 3.2 15.3 - - + +
140B MET 4.8 1.5 + - - +
1007B SO4 3.2 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 4.0 3.6 - - - +
108B ALA* 1.3 76.2 - - - +
110B GLU* 1.3 62.1 + - - +
112B VAL* 3.3 6.5 + - - +
113B GLN* 2.9 45.6 + - - +
124B GLU* 3.1 16.9 + - - -
1007B SO4 2.9 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 3.4 16.9 - - - +
99B ASP* 3.6 0.7 - - - +
100B LYS* 3.1 29.9 + - + +
101B ASN* 2.6 19.4 + - - +
105B LYS 3.2 5.5 - - - +
106B ILE* 3.3 5.8 - - + -
107B GLU* 2.9 30.6 + - - +
109B SER* 1.3 81.8 + - - +
111B ILE* 1.3 60.5 + - - +
113B GLN* 3.5 11.5 + - - +
114B SER* 2.9 35.0 + - - -
1003B CA 2.4 31.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.9 7.9 - - + -
106B ILE* 4.0 17.5 - - + -
107B GLU 3.4 3.3 + - - +
108B ALA 3.0 7.9 + - - +
110B GLU* 1.3 74.1 - - - +
112B VAL* 1.3 62.1 + - - +
114B SER* 3.4 4.2 + - - -
115B LEU* 2.9 45.0 + - + +
122B ILE* 3.9 11.9 - - + -
127B ALA* 3.8 20.4 - - + +
130B ILE* 4.1 24.7 - - + -
131B LEU* 3.6 33.2 - - + -
147B TRP* 6.1 0.4 - - + -
166B TRP* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 2.9 18.8 + - - +
109B SER* 3.4 9.0 - - - +
111B ILE* 1.3 77.0 - - - +
113B GLN* 1.3 60.7 + - + +
115B LEU* 3.8 1.9 - - - +
116B GLN* 2.9 35.5 + - + +
120B LEU 4.5 1.4 - - - +
122B ILE* 3.8 27.6 + - + +
123B SER 3.7 24.2 - - - +
124B GLU* 4.0 16.8 - - - +
127B ALA* 3.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS* 4.0 25.0 - - - +
109B SER* 2.9 36.1 + - - +
110B GLU* 3.8 11.9 - - - +
112B VAL* 1.3 76.6 - - + +
114B SER* 1.3 64.8 + - - +
116B GLN* 3.0 9.7 + - - +
117B THR* 2.9 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B SER 4.1 0.2 + - - -
98B LEU* 3.3 33.5 - - - +
100B LYS* 3.4 26.1 + - - +
110B GLU 2.9 21.8 + - - -
111B ILE* 3.8 3.4 - - - -
113B GLN* 1.3 76.4 - - - +
115B LEU* 1.3 64.4 + - - +
117B THR* 2.5 26.2 + - - -
118B LEU* 3.4 12.4 + - - +
159B ILE* 5.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 5.7 0.9 - - + -
111B ILE* 2.9 30.6 + - + +
112B VAL 4.0 2.7 - - - +
114B SER* 1.3 83.3 - - - +
116B GLN* 1.3 56.1 + - - +
118B LEU* 3.1 12.9 + - + +
119B GLY 3.2 0.2 + - - -
120B LEU* 2.7 50.5 + - + +
122B ILE* 3.6 38.6 - - + -
130B ILE* 5.0 1.6 - - + -
159B ILE* 5.5 4.0 - - + -
163B ILE* 3.7 30.3 - - + -
166B TRP* 4.4 8.7 - - + -
174B ILE* 4.3 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 2.9 21.8 + - + +
113B GLN* 3.0 13.4 + - - +
115B LEU* 1.3 78.3 - - - +
117B THR* 1.3 62.5 + - + +
119B GLY* 3.1 14.4 + - - -
120B LEU 3.2 10.3 + - - +
121B THR* 3.1 40.1 + - - +
122B ILE 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS* 5.5 8.6 + - - +
113B GLN* 2.9 19.7 + - + +
114B SER* 2.5 24.2 + - - -
116B GLN* 1.3 76.6 - - + +
118B LEU* 1.3 65.9 + - - +
119B GLY 3.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B SER* 3.6 14.4 - - - +
115B LEU* 3.1 10.8 + - + +
117B THR* 1.3 84.9 + - - +
119B GLY* 1.3 61.7 + - - +
120B LEU* 3.4 10.4 + - + +
159B ILE* 4.2 25.6 - - + -
160B GLU* 4.8 17.7 - - + +
163B ILE* 3.7 28.9 - - + -
----------------------------------------------------------
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