Contacts of the strand formed by residues 122 - 129 (chain A) in PDB entry 1ZUQ
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 GLY 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.8 7.5 - - - +
120A GLY 4.1 0.2 + - - -
121A SER* 1.3 79.8 - - - +
123A TRP* 1.3 64.8 + - - -
140A CYS 3.2 12.3 - - - -
142A ASN 3.5 11.0 - - - -
160A VAL* 2.8 37.5 + - - +
161A TRP* 3.4 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.4 45.7 - - + +
74A HIS* 3.7 18.8 - + - -
77A PHE* 3.6 37.0 - + + -
118A VAL* 4.1 6.3 - - - +
122A GLY* 1.3 79.3 - - - -
124A GLY* 1.3 61.4 + - - +
125A TRP* 3.1 36.9 - + + +
139A ALA* 3.1 4.7 - - - +
140A CYS* 2.8 38.4 + - + +
142A ASN 3.3 15.1 + - - -
143A GLN* 3.0 18.3 + - - -
144A ASP 5.4 1.8 - - - -
157A GLY 4.4 1.1 - - - -
158A ILE 3.3 11.7 - - - -
159A ASP* 3.4 47.4 + - + -
160A VAL* 4.0 1.1 - - - +
161A TRP* 3.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 4.1 8.9 - - - +
114A ALA* 4.9 1.1 - - - -
115A SER* 3.7 29.0 + - - +
123A TRP* 1.3 75.0 - - - +
125A TRP* 1.3 65.6 + - - -
138A ALA 3.6 4.7 - - - -
139A ALA* 4.2 4.3 - - - -
158A ILE 3.0 32.5 + - - -
160A VAL* 4.8 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.7 28.8 + - + -
76A ILE* 3.8 33.4 - - + -
77A PHE 5.3 0.2 - - - -
111A LEU* 3.9 8.9 - - - +
123A TRP* 3.1 45.1 - + + +
124A GLY* 1.3 80.7 - - - -
126A LEU* 1.3 59.7 + - - +
127A GLY 3.9 0.4 - - - -
137A ILE* 3.3 11.1 - - - +
138A ALA 2.6 37.8 + - - +
140A CYS* 4.0 24.1 - - - +
144A ASP 5.1 0.6 + - - -
146A LEU* 3.8 30.9 - - + +
154A PRO* 3.4 31.6 - - + -
156A LEU 3.2 24.2 - - - -
157A GLY* 3.3 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 5.7 2.5 - - + -
97A ILE* 4.3 12.3 - - + -
101A PHE* 3.9 26.2 - - + -
107A PHE* 3.8 38.8 - - + -
111A LEU* 4.5 4.0 - - + +
125A TRP* 1.3 73.5 - - - +
127A GLY* 1.3 66.8 + - - +
135A LEU* 4.3 5.6 - - + -
136A GLN 4.0 1.1 - - - +
137A ILE* 4.2 5.6 - - + -
154A PRO* 3.9 2.1 - - - +
155A LEU* 2.9 47.2 + - + +
156A LEU* 2.8 29.1 + - + +
186A TRP* 4.8 3.4 - - + -
189A VAL* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TRP 3.9 1.0 - - - -
126A LEU* 1.3 75.8 - - - +
128A PHE* 1.3 60.7 + - - -
135A LEU* 3.5 11.8 - - - +
136A GLN* 2.8 36.6 + - - -
146A LEU* 4.0 13.0 - - - +
152A LEU* 4.6 6.1 - - - -
153A ILE 3.0 13.0 - - - -
155A LEU* 4.2 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY* 1.3 72.9 - - - -
129A ASN* 1.3 58.5 + - - +
130A LYS* 3.3 35.3 + - + -
133A GLY* 3.8 20.0 - - - -
134A HIS* 3.5 27.1 - - - -
135A LEU* 4.4 11.2 - - + -
152A LEU* 3.8 6.2 - - - +
153A ILE* 2.9 33.3 + - + +
155A LEU* 4.3 7.4 - - + -
193A TYR* 5.2 11.4 - + - -
196A CYS* 3.3 48.0 - - + -
197A LYS* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY 4.2 0.4 - - - -
128A PHE* 1.3 71.9 - - - +
130A LYS* 1.3 51.5 + - - +
131A GLU* 3.0 14.7 + - - +
132A ARG* 2.6 41.1 + - - +
133A GLY* 2.5 37.6 + - - -
134A HIS* 2.7 30.4 + - + +
136A GLN* 2.8 27.7 + - - +
152A LEU* 3.8 15.1 - - + +
----------------------------------------------------------
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