Contacts of the strand formed by residues 150 - 156 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 2.9 6.4 - - - -
127A LYS* 2.6 65.1 + - + +
145A LEU* 5.5 0.2 - - - -
148A ASN 5.1 2.9 - - - +
149A LYS* 1.3 74.2 - - - +
151A PRO* 1.3 68.1 - - + +
152A LEU* 3.7 6.9 - - + +
189A GLN 5.7 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 4.3 12.6 - - + -
76A PHE* 3.3 31.6 - - + -
124A TRP* 3.8 24.2 - - + -
125A LEU 3.8 5.6 - - - +
126A VAL* 4.0 6.7 - - + -
144A PRO* 4.8 4.9 - - + -
145A LEU* 3.9 20.9 - - + -
149A LYS 3.4 10.2 - - - +
150A LYS* 1.3 84.5 - - + +
152A LEU* 1.3 65.3 + - - +
189A GLN* 3.8 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE* 3.5 14.2 - - - -
80A CYS* 4.2 2.4 - - - -
92A LEU* 5.0 1.6 - - + -
125A LEU* 2.8 25.7 + - + +
126A VAL 4.0 8.3 - - - -
127A LYS* 4.1 8.5 - - + +
133A LEU* 3.4 33.2 - - + -
150A LYS* 3.7 15.5 - - + +
151A PRO* 1.3 83.4 - - - +
153A LEU* 1.3 58.4 + - - +
185A PHE* 4.3 1.0 - - - -
186A VAL* 3.6 35.6 - - + +
189A GLN* 3.8 11.9 - - - +
190A PHE* 3.7 44.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE* 3.9 3.6 - - - -
80A CYS* 3.7 26.9 - - + +
106A PHE* 4.3 13.9 - - + -
110A PHE* 4.0 23.8 - - + -
124A TRP* 3.3 6.9 - - - -
125A LEU* 3.0 35.9 + - + +
152A LEU* 1.3 79.0 - - - +
154A THR* 1.3 72.4 + - - +
155A PHE* 4.2 14.4 - - + -
178A TRP* 4.3 16.6 - - + -
181A VAL* 4.2 15.9 - - + -
183A TRP* 4.9 2.9 - - + -
186A VAL* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN 4.3 1.3 - - - +
76A PHE* 3.9 11.7 - - + -
77A TYR* 3.6 40.9 - - + +
80A CYS* 3.6 13.4 - - - +
81A LEU* 5.5 0.3 - - - +
110A PHE* 4.6 0.4 - - - -
122A TRP* 3.4 27.3 - - + +
123A ALA 2.9 17.4 + - - -
124A TRP* 3.5 25.1 - - + -
153A LEU* 1.3 78.1 - - - +
155A PHE* 1.3 72.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 4.2 4.3 - + - -
81A LEU* 5.5 3.6 - - + -
110A PHE* 3.6 31.6 - + + -
114A ALA* 4.2 7.2 - - + -
122A TRP* 3.5 3.6 - - - -
123A ALA* 3.1 33.5 + - + +
153A LEU* 4.2 8.3 - - + -
154A THR* 1.3 86.2 - - - +
156A ASP* 1.3 61.6 + - - +
157A VAL* 3.5 10.7 + - + +
174A VAL* 3.9 27.6 - - + -
177A LEU* 3.5 36.3 - - + -
178A TRP* 3.8 31.9 - + - -
181A VAL* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 2.8 10.7 + - - -
74A HIS* 3.4 2.4 + - - -
77A TYR* 3.5 26.1 - - + -
121A GLY 3.5 0.9 - - - +
122A TRP* 3.3 29.4 - - + -
155A PHE* 1.3 69.2 - - - +
157A VAL* 1.3 62.5 + - - +
158A TRP* 3.1 26.0 + - - -
160A HIS* 3.6 0.2 + - - -
161A ALA* 3.4 11.9 - - + +
173A TYR* 2.7 31.7 + - - -
1001A FE 1.9 32.8 - - - -
----------------------------------------------------------
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