Contacts of the strand formed by residues 150 - 156 (chain B) in PDB entry 3H1S
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 150 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 3.2 3.5 - - - -
127B LYS* 2.9 59.6 + - + +
145B LEU* 5.0 2.9 - - + -
148B ASN 4.4 0.2 + - - -
149B LYS* 1.3 71.0 - - - +
151B PRO* 1.3 75.4 - - + +
152B LEU* 3.9 2.8 - - + +
188B GLU 4.8 0.8 + - - -
189B GLN* 3.0 53.4 + - - +
191B ALA 3.8 13.3 + - - -
192B ASP* 4.5 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 4.1 23.1 - - + -
76B PHE* 3.3 29.0 - - + -
124B TRP* 3.6 31.2 - - + -
125B LEU 3.9 4.7 - - - +
126B VAL* 4.2 4.9 - - + -
144B PRO* 4.3 7.0 - - + -
145B LEU* 3.8 15.9 - - + -
149B LYS 3.4 9.6 - - - +
150B LYS* 1.3 92.0 - - + +
152B LEU* 1.3 64.5 + - - +
189B GLN* 3.8 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 3.6 12.0 - - - -
80B CYS* 4.3 1.9 - - - -
92B LEU* 4.9 1.6 - - + -
125B LEU* 2.7 31.7 + - + +
126B VAL 4.1 4.3 - - - -
127B LYS* 4.0 11.0 - - + +
133B LEU* 3.6 31.2 - - + -
150B LYS* 3.9 13.2 - - + +
151B PRO* 1.3 79.1 - - - +
153B LEU* 1.3 57.6 + - - +
185B PHE* 4.3 2.1 - - - -
186B VAL* 3.4 38.1 + - + +
189B GLN* 3.4 37.2 - - + +
190B PHE* 3.6 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 3.7 4.2 - - - -
80B CYS* 3.7 25.4 - - + -
106B PHE* 4.3 13.5 - - + -
110B PHE* 3.9 23.7 - - + -
124B TRP* 3.3 6.8 - - - +
125B LEU* 2.9 36.4 + - + +
152B LEU* 1.3 78.5 - - - +
154B THR* 1.3 68.3 + - - +
155B PHE* 4.0 20.2 - - + -
178B TRP* 4.2 18.6 - - + -
181B VAL* 4.0 16.4 - - + -
183B TRP* 5.2 2.2 - - + -
186B VAL* 3.8 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN 4.1 1.6 - - - +
76B PHE* 3.7 18.2 - - + -
77B TYR* 3.7 36.1 - - + +
80B CYS* 3.5 14.4 - - - +
81B LEU* 5.5 0.2 - - - +
122B TRP* 3.5 24.3 - - + +
123B ALA 2.8 16.9 + - - -
124B TRP* 3.4 30.2 - - + -
153B LEU* 1.3 76.5 - - - +
155B PHE* 1.3 70.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 4.4 4.0 - + - -
81B LEU* 5.5 3.8 - - + -
110B PHE* 3.5 28.0 - + + -
114B ALA* 4.4 4.7 - - + -
122B TRP* 3.5 3.3 - - - -
123B ALA* 2.9 36.2 + - + +
153B LEU* 4.0 11.0 - - + -
154B THR* 1.3 82.4 - - - +
156B ASP* 1.3 62.7 + - - +
157B VAL* 3.5 10.6 + - + +
174B VAL* 4.1 29.2 - - + -
177B LEU* 3.6 32.1 - - + -
178B TRP* 3.8 37.7 - + - -
181B VAL* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B HIS* 2.9 10.4 + - - -
74B HIS* 3.4 2.9 + - - -
77B TYR* 3.6 23.0 - - + -
121B GLY 3.6 0.3 - - - +
122B TRP* 3.4 29.5 - - + -
155B PHE* 1.3 70.1 - - - +
157B VAL* 1.3 59.3 + - - +
158B TRP* 3.0 37.1 + - - +
161B ALA* 3.7 12.9 - - + +
173B TYR* 2.6 32.7 + - - -
1001B FE 2.0 31.3 - - - -
----------------------------------------------------------
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