Contacts of the strand formed by residues 135 - 140 (chain B) in PDB entry 1ZQ1
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 135 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLY* 3.2 18.9 - - - -
88B LYS* 2.9 42.4 + - - +
91B LEU* 3.6 23.0 - - - +
92B PRO 2.6 8.8 + - - +
93B GLU* 3.2 32.5 - - - +
94B VAL 2.9 26.8 + - - +
131B PHE* 5.0 5.5 + - - -
134B ALA* 1.3 70.8 + - - +
136B VAL* 1.3 62.3 + - - +
137B LYS* 3.6 6.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 4.8 0.9 - - - +
85B ILE* 5.3 2.9 + - - +
94B VAL* 3.3 8.7 - - + +
96B ILE* 3.4 33.7 - - + -
120B ALA* 4.2 3.8 - - - +
123B LEU* 4.3 6.1 - - + -
130B ILE* 3.8 29.2 - - + +
131B PHE* 3.7 28.2 - - + -
134B ALA 3.4 12.2 + - - +
135B ASN* 1.3 72.1 - - - +
137B LYS* 1.3 63.0 + - - +
138B PRO* 3.2 21.7 - - + +
223B VAL* 4.5 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.9 18.6 - - + -
93B GLU* 2.7 42.0 + - + +
94B VAL 2.8 11.1 + - - +
95B THR* 3.1 19.3 - - + +
96B ILE 2.9 20.8 + - - -
135B ASN* 4.3 6.7 - - + +
136B VAL* 1.3 76.0 - - - +
138B PRO* 1.3 63.9 - - - +
169B ASP* 4.1 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA 5.1 0.8 - - - +
84B LEU* 3.5 26.7 - - + +
96B ILE* 3.5 10.1 - - + +
118B PHE* 3.2 40.6 - - + +
120B ALA* 3.9 21.8 - - + +
123B LEU* 3.9 16.4 - - + -
136B VAL* 3.2 15.5 - - + +
137B LYS* 1.3 84.5 - - - +
139B LYS* 1.3 59.2 + - - +
140B LEU 4.1 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B THR* 4.1 20.2 - - + -
96B ILE 2.9 9.3 + - - -
97B ILE* 3.5 8.9 - - + +
98B GLY 3.0 18.9 + - - -
118B PHE* 4.0 3.1 - - - -
137B LYS 3.5 1.0 + - - -
138B PRO* 1.3 75.1 - - - +
140B LEU* 1.3 63.5 + - - +
141B LEU* 3.2 6.7 + - - +
160B GLU* 2.7 37.6 + - + +
163B LYS* 3.0 28.5 - - - +
164B ALA* 6.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLY* 3.6 11.2 - - - +
100B GLY 5.6 0.4 - - - +
118B PHE* 3.9 25.4 - - + -
138B PRO 4.1 1.4 + - - -
139B LYS* 1.3 75.9 - - - +
141B LEU* 1.3 63.9 + - - +
142B PHE* 3.2 26.7 - - - +
143B ASN* 4.0 10.8 - - + +
----------------------------------------------------------
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