Contacts of the helix formed by residues 110 - 125 (chain B) in PDB entry 1ZB8
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 110 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY 3.8 6.8 + - - +
109B MET* 1.3 77.0 - - - +
111B ARG* 1.3 61.5 + - - +
112B SER* 4.2 14.6 - - - +
113B MET* 3.2 9.2 + - + -
114B LEU* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL 3.5 20.2 + - - -
107B SER* 5.3 0.6 - - - +
108B GLY 4.9 2.2 - - - +
109B MET 2.7 24.7 + - - +
110B GLU* 1.3 74.0 + - - +
112B SER* 1.3 58.1 + - - +
114B LEU* 3.6 26.9 - - - +
115B GLN* 2.8 32.2 + - - +
141B LEU* 3.5 18.4 - - + +
142B ILE 2.9 37.6 + - - +
143B ASP* 3.8 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLU* 4.2 9.4 - - - +
111B ARG* 1.3 78.6 - - - +
113B MET* 1.3 59.9 + - - +
115B GLN* 3.5 7.8 - - - +
116B THR* 3.1 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 3.8 45.5 - - + -
109B MET* 4.0 14.1 - - + -
110B GLU* 3.2 16.0 + - + +
112B SER* 1.3 79.1 + - - +
114B LEU* 1.3 65.6 + - - +
115B GLN 3.1 1.1 - - - -
116B THR* 3.0 15.3 + - + -
117B LEU* 2.9 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 4.8 5.6 - - + -
104B ILE* 3.6 28.3 - - + +
106B VAL* 3.5 37.5 - - + +
109B MET* 3.7 16.6 - - + -
110B GLU 2.9 16.5 + - - +
111B ARG* 3.6 35.9 - - - +
113B MET* 1.3 75.1 - - - +
115B GLN* 1.3 57.5 + - - +
117B LEU* 3.3 3.7 + - + -
118B VAL* 2.8 52.1 + - + +
141B LEU* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ARG 2.8 22.1 + - - +
112B SER* 3.5 9.9 - - - +
114B LEU* 1.3 72.6 - - - +
116B THR* 1.3 58.7 + - - +
118B VAL* 4.4 5.7 - - - +
119B ASP* 3.0 67.5 + - - +
139B LEU* 5.3 6.3 + - - +
141B LEU* 3.6 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 5.4 1.1 - - - +
112B SER 3.1 11.8 + - - -
113B MET* 3.0 25.9 + - + +
115B GLN* 1.3 79.9 - - - +
117B LEU* 1.3 67.4 + - + +
119B ASP* 3.4 5.3 + - - +
120B LYS* 3.0 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 3.7 11.9 - - + +
69B VAL* 3.3 13.3 - - + +
70B ALA* 3.9 39.5 - - + +
73B GLU* 4.4 20.9 - - + -
75B VAL* 4.1 9.4 - - + -
77B LEU* 3.9 16.2 - - + -
106B VAL* 6.2 0.2 - - + -
109B MET* 3.9 18.6 - - + -
113B MET* 2.9 32.6 + - - +
114B LEU* 3.9 5.8 - - + +
116B THR* 1.3 80.1 - - + +
118B VAL* 1.3 51.2 + - - +
120B LYS* 3.3 2.0 + - + -
121B ALA* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 3.5 5.6 - - + -
66B LEU* 3.7 13.0 - - + -
104B ILE* 3.8 38.1 - - + -
114B LEU* 2.8 26.7 + - + +
115B GLN* 3.8 8.3 - - - +
117B LEU* 1.3 69.5 - - - +
119B ASP* 1.3 61.1 + - - +
121B ALA 3.3 0.5 + - - -
122B HIS* 2.9 28.6 + - - +
139B LEU* 3.7 32.8 - - + -
141B LEU* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLN* 3.0 47.0 + - - +
116B THR* 3.8 5.1 - - - +
118B VAL* 1.3 75.0 - - - +
120B LYS* 1.3 62.0 + - + +
122B HIS* 3.6 8.5 + - - +
123B ARG* 3.3 19.8 + - - +
139B LEU* 3.9 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 3.8 16.8 - - + +
73B GLU* 3.5 44.2 + - + +
116B THR* 3.0 41.3 + - + +
117B LEU* 3.6 6.1 - - - +
119B ASP* 1.3 76.1 - - + +
121B ALA* 1.3 64.1 + - - +
123B ARG* 3.0 17.5 + - - +
124B VAL* 3.2 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 3.8 11.2 - - + -
65B ALA* 3.7 4.6 - - + +
66B LEU* 3.6 37.9 - - + +
69B VAL* 3.7 10.9 - - + +
117B LEU 2.8 21.2 + - - +
118B VAL 3.3 4.5 + - - +
120B LYS* 1.3 72.7 - - - +
122B HIS* 1.3 51.1 + - - +
124B VAL* 3.1 6.0 + - - +
125B CYS* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 3.8 1.3 + - - -
62B PHE* 3.5 9.9 - - + -
118B VAL 2.9 17.1 + - - +
119B ASP* 3.7 7.0 - - - +
121B ALA* 1.3 74.6 - - - +
123B ARG* 1.3 57.6 + - - +
125B CYS 4.1 0.2 - - - -
128B SER* 2.6 52.7 + - - -
132B ARG* 2.9 39.5 + - - -
137B VAL* 3.7 35.4 + - + +
139B LEU* 3.6 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASP 3.3 11.5 + - - +
120B LYS* 3.0 13.3 + - - +
122B HIS* 1.3 76.8 - - - +
124B VAL* 1.3 63.6 + - + +
129B ASN* 3.2 24.9 + - - +
132B ARG* 3.5 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLY 4.0 20.2 - - - +
96A PHE 4.3 6.9 + - - +
270A PE4 3.9 27.4 - - - +
65B ALA* 4.2 7.9 - - + +
68B PHE* 4.8 10.5 - - + -
69B VAL* 3.7 27.1 - - + -
120B LYS 3.2 6.8 + - - +
121B ALA* 3.2 14.6 - - - +
123B ARG* 1.3 82.6 - - + +
125B CYS* 1.3 63.1 + - - +
126B PRO* 3.1 10.6 - - - +
129B ASN* 4.0 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 3.6 33.4 - - - -
61B OCS 3.1 25.1 - - - +
62B PHE* 4.0 15.5 - - + -
65B ALA* 4.1 4.7 - - + -
121B ALA 2.8 19.7 + - - +
122B HIS 4.1 0.2 - - - -
123B ARG 3.6 1.0 - - - -
124B VAL* 1.3 72.2 - - - +
126B PRO* 1.4 60.9 - - - +
127B TYR* 3.7 9.0 - - - -
128B SER* 3.0 16.6 + - - +
129B ASN* 2.9 33.7 + - - -
----------------------------------------------------------
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