Contacts of the strand formed by residues 140 - 146 (chain A) in PDB entry 5IZL
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 LYS 140 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP 3.6 5.1 + - - +
112A LEU* 3.4 19.9 - - + -
113A MET* 3.2 26.6 + - - +
138A CYS* 4.2 2.3 - - - +
139A GLN* 1.3 86.9 - - + +
141A LEU* 1.3 62.3 + - - +
176A PHE* 3.7 7.9 - - - -
211A SER 5.4 0.4 + - - -
212A GLN* 2.9 50.3 + - - +
214A SER* 3.1 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.8 0.9 - - - -
113A MET* 3.4 36.8 - - + +
115A LEU* 3.9 19.7 - - + -
131A LEU* 4.2 7.4 - - + -
140A LYS* 1.3 78.4 - - - +
142A VAL* 1.3 81.5 + - - +
143A VAL* 4.0 17.7 - - + -
171A LEU* 4.1 15.0 - - + -
176A PHE* 3.5 48.9 - - + -
179A ALA* 3.6 18.2 - - + +
180A PRO* 3.7 5.5 - - - +
212A GLN* 4.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.3 20.6 - - + -
113A MET 3.1 8.2 + - - +
114A MET* 3.3 10.4 - - + -
115A LEU 3.0 23.6 + - - -
141A LEU* 1.3 82.5 - - - +
143A VAL* 1.3 63.0 + - - +
144A VAL* 3.9 11.3 + - + -
180A PRO* 3.9 17.3 - - + -
182A ILE* 3.3 31.0 - - + -
205A LEU* 4.4 6.5 - - + -
208A LEU* 4.7 3.6 - - + -
209A LEU* 4.4 5.6 - - + -
212A GLN* 4.4 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.6 10.8 - - + +
117A ILE* 4.0 22.9 - - + -
141A LEU* 4.0 22.2 - - + -
142A VAL* 1.3 74.3 - - - +
144A VAL* 1.3 61.2 + - - +
145A LEU* 4.1 13.0 - - + -
167A MET* 4.2 19.7 - - + -
171A LEU* 4.1 18.2 - - + -
179A ALA* 5.1 0.2 - - + -
180A PRO 2.9 15.7 + - - +
181A ILE* 3.4 14.3 - - + -
182A ILE* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 17.5 - - + -
114A MET* 4.1 29.4 - - + -
115A LEU 2.9 13.6 + - - +
116A VAL* 3.5 10.7 - - + +
117A ILE* 2.8 27.9 + - - -
142A VAL* 4.0 16.2 - - + -
143A VAL* 1.3 78.1 - - - +
145A LEU* 1.3 66.2 + - - +
146A ASN* 3.5 1.6 + - + +
182A ILE* 3.5 5.2 - - + +
184A VAL* 3.7 28.0 - - + -
205A LEU* 4.3 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.7 28.5 - - + -
119A VAL* 3.9 15.3 - - + -
143A VAL* 4.1 10.3 - - + -
144A VAL* 1.3 72.6 - - - +
146A ASN* 1.3 60.2 + - - +
148A ILE* 3.5 5.6 - - + +
160A ILE* 4.4 15.0 - - + -
163A MET* 4.0 29.4 - - + -
164A THR* 4.0 15.5 - - - +
167A MET* 4.6 3.1 - - + -
181A ILE* 3.7 23.1 - - + -
182A ILE 2.7 17.6 + - - +
183A PRO* 3.4 7.5 - - + +
184A VAL* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER 3.0 27.2 + - - +
19A GLY* 3.8 9.0 + - - -
23A LEU* 5.2 1.8 - - - -
116A VAL* 4.0 12.6 - - + -
117A ILE 2.8 11.1 + - - +
118A ASP* 4.7 0.2 - - - -
119A VAL* 2.8 28.2 + - - +
144A VAL* 3.5 5.4 + - + +
145A LEU* 1.3 73.7 - - - +
147A LYS* 1.3 75.5 + - - +
148A ILE* 3.5 1.8 - - - -
184A VAL* 2.9 16.7 - - - +
186A ALA* 2.9 36.8 + - - +
1002A GCP 3.6 21.6 + - - -
----------------------------------------------------------
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