Contacts of the strand formed by residues 156 - 161 (chain T) in PDB entry 1V2J
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 156 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16T ILE* 3.8 22.2 - - + +
19T GLY 5.3 2.0 + - - -
20T TYR* 3.3 17.8 - - - +
21T THR* 2.9 25.4 + - - +
22T CYS* 3.2 5.3 - - - -
139T SER* 3.2 8.3 - - - -
140T GLY 3.0 37.0 + - - +
144T THR* 4.5 14.4 - - + -
152T PRO* 4.0 30.3 - - + -
154T VAL* 3.9 16.1 - - - +
155T LEU* 1.3 74.8 - - - +
157T CYS* 1.3 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 157 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16T ILE* 4.3 1.3 - - - -
19T GLY* 3.1 6.3 - - - -
20T TYR* 2.6 70.1 + - + +
22T CYS* 2.0 45.3 - - - -
27T VAL* 3.8 15.5 - - - -
137T LEU* 4.0 13.7 - - + -
138T ILE 3.5 2.9 - - - -
139T SER* 4.0 7.4 - - - -
156T LYS* 1.3 72.6 - - - +
158T LEU* 1.3 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16T ILE* 3.7 11.9 - - + -
17T VAL 4.4 1.1 - - - +
18T GLY 4.2 10.8 - - - +
19T GLY* 4.4 3.1 - - - -
20T TYR* 4.3 2.9 - - + -
136T CYS 3.6 0.5 - - - +
137T LEU* 3.5 3.3 - - - +
138T ILE* 2.8 59.6 + - + +
157T CYS* 1.3 76.1 - - - +
159T LYS* 1.3 75.7 + - - +
160T ALA* 3.8 7.5 + - + -
184T TYR* 4.5 0.9 - - + -
188T LYS* 3.5 39.7 - - + +
189T ASP* 3.6 41.5 - - - +
190T SER* 4.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T TYR* 3.1 38.8 + - + +
135T GLN* 4.1 17.0 - - + +
136T CYS 3.2 8.5 - - - +
137T LEU* 4.4 7.4 - - + -
158T LEU* 1.3 79.4 - - - +
160T ALA* 1.3 55.2 + - - +
184T TYR* 2.5 30.3 + - - -
188T LYS* 4.0 2.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135T GLN* 4.0 3.7 + - - -
136T CYS* 2.6 46.8 + - - +
138T ILE* 3.8 26.2 - - + -
158T LEU* 3.8 6.4 + - + -
159T LYS* 1.3 76.5 - - - +
161T PRO* 1.3 68.1 - - + +
183T ALA* 4.7 2.7 - - + +
184T TYR* 3.8 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 161 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133T GLY* 4.3 10.3 - - - +
134T THR 3.2 7.9 - - - +
135T GLN* 3.5 20.9 - - - +
160T ALA* 1.3 90.0 - - + +
162T ILE* 1.3 67.0 + - - +
163T LEU* 3.6 8.1 + - + +
183T ALA* 3.1 4.5 - - - +
184T GLY* 3.1 60.6 + - + +
----------------------------------------------------------
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