Contacts of the strand formed by residues 144 - 149 (chain L) in PDB entry 3HI6
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 144 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143L ALA* 1.3 73.4 - - - +
145L VAL* 1.3 66.5 + - - +
146L GLN* 3.2 45.9 + - + +
194L GLU 3.5 1.2 - - - +
195L VAL* 3.3 6.9 - - - +
196L THR* 2.9 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133L CYS* 4.6 0.7 - - - -
135L LEU* 3.7 33.7 - - + -
143L ALA 5.2 1.8 - - - -
144L LYS* 1.3 82.2 + - - +
146L GLN* 1.3 64.2 + - - +
147L TRP* 4.2 11.1 + - + +
158L SER* 5.7 0.7 + - - -
160L GLU* 3.7 25.0 + - - +
174L LEU* 4.0 10.3 - - + -
176L SER* 3.7 22.8 + - - +
193L CYS* 3.6 29.4 - - - -
194L GLU 3.5 2.9 - - - +
195L VAL* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144L LYS* 3.2 42.5 + - + +
145L VAL* 1.3 73.2 - - - +
147L TRP* 1.3 62.4 + - - +
148L LYS* 4.1 4.1 + - + +
153L LEU* 3.3 39.7 - - + +
154L GLN 6.0 0.2 - - - -
192L ALA 3.8 0.3 - - - +
193L CYS* 3.6 2.9 - - - -
194L GLU* 2.8 60.8 + - + +
196L THR* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 147 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116L ILE* 3.9 17.0 - - + -
131L VAL* 3.6 42.4 - - + -
132L VAL 4.0 1.3 - - - -
133L CYS* 3.4 35.7 - - + -
145L VAL* 4.2 7.0 - - + +
146L GLN* 1.3 75.7 - - - +
148L LYS* 1.3 63.4 + - - +
153L LEU* 3.5 8.7 - - - +
154L GLN* 2.9 50.2 + - + +
158L SER* 3.9 23.9 - - - -
176L SER* 2.8 37.3 + - - -
178L LEU* 3.7 24.2 - - + +
191L TYR* 5.3 1.8 - - + -
192L ALA 3.4 21.3 - - - -
193L CYS* 4.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146L GLN* 4.1 4.9 + - + +
147L TRP* 1.3 79.0 - - - +
149L VAL* 1.3 64.1 + - - +
150L ASP 4.1 0.2 - - - -
151L ASN* 3.0 43.5 + - - +
152L ALA 3.3 11.2 - - - +
153L LEU* 4.2 19.3 - - + +
190L VAL 3.5 3.1 - - - +
191L TYR* 3.5 1.4 - - - -
192L ALA* 2.8 52.9 + - + +
194L GLU* 5.1 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148L LYS* 1.3 75.3 - - - +
150L ASP* 1.3 64.7 + - - +
152L ALA* 2.9 35.2 + - - +
154L GLN* 3.7 31.4 - - + +
178L LEU* 4.1 11.2 - - + -
180L LEU* 4.8 4.9 - - + -
188L HIS* 3.4 44.6 + - + +
190L VAL 3.3 2.7 - - - -
191L TYR* 3.6 31.6 - - + -
----------------------------------------------------------
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