Contacts of the strand formed by residues 131 - 139 (chain B) in PDB entry 3ULA
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 TYR 131 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 3.6 29.8 - - + -
80B ILE* 6.0 1.1 - - + -
81B THR 3.7 2.0 - - - -
82B VAL* 3.4 46.0 - - + -
124B ILE* 3.7 22.1 - - + +
127B SER* 2.5 43.3 + - - -
129B GLY 3.9 14.4 - - - -
130B LYS* 1.3 75.6 - - - +
132B LYS* 1.3 60.3 + - - +
133B CYS* 4.1 0.9 - - + -
151B PHE 3.4 1.2 - - - +
152B VAL* 3.3 4.3 - - - -
153B ILE* 2.7 69.5 + - + +
155B HIS* 5.7 0.2 - - + -
401C E55 4.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR 3.4 4.0 - - - +
80B ILE* 3.6 0.8 - - - -
81B THR* 2.7 57.1 + - + +
130B LYS* 4.0 8.4 + - - +
131B TYR* 1.3 74.0 - - - +
133B CYS* 1.3 63.7 + - - +
134B VAL* 5.0 10.1 - - + -
150B GLU* 4.7 20.2 - - + +
151B PHE 3.3 6.1 - - - +
152B VAL* 4.3 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 4.4 4.3 - - - -
79B TYR 3.3 2.2 - - - -
80B ILE* 3.9 34.1 - - + -
131B TYR 4.1 0.6 - - - -
132B LYS* 1.3 75.6 - - - +
134B VAL* 1.3 72.2 + - - +
135B VAL* 3.9 7.4 + - - +
149B LEU 3.5 1.6 - - - +
150B GLU* 4.6 0.4 - - - -
151B PHE* 2.7 46.5 + - + +
401C E55 3.8 41.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B CYS* 5.7 0.2 - - + -
77B ASN 3.6 0.5 - - - +
78B LEU* 3.6 4.7 - - - -
79B TYR* 3.0 65.3 + - + +
132B LYS* 5.0 9.6 - - + -
133B CYS* 1.3 75.9 - - - +
135B VAL* 1.3 67.4 + - - +
136B GLU 4.0 2.0 - - - +
148B CYS* 3.5 28.0 - - - -
149B LEU 3.3 4.0 - - - -
150B GLU* 3.7 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 4.9 10.5 - - + -
77B ASN 3.8 3.8 - - - -
78B LEU* 3.8 20.6 - - + -
133B CYS* 3.9 18.4 - - - +
134B VAL* 1.3 80.4 - - - +
136B GLU* 1.3 62.8 + - - +
137B ALA 3.3 3.8 + - - -
147B PHE* 3.8 13.0 - - + -
148B CYS* 3.6 2.5 - - - -
149B LEU* 2.9 44.1 + - + +
151B PHE* 4.2 11.2 - - + -
401C E55 4.4 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B TYR 3.6 1.6 - - - +
76B PHE* 3.5 4.5 - - - -
77B ASN* 3.1 48.8 + - + +
79B TYR* 3.4 28.9 + - + -
89B LYS* 4.4 1.2 + - - -
134B VAL* 4.0 1.0 - - - +
135B VAL* 1.3 71.9 - - - +
137B ALA* 1.3 61.3 + - - +
138B ILE* 3.8 12.3 + - + +
145B MET* 4.2 28.5 - - + +
147B PHE 3.6 9.2 - - - +
148B CYS* 4.2 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 4.6 5.2 - - + -
75B TYR 3.9 3.6 - - - -
76B PHE* 4.0 15.9 - - + -
135B VAL 3.3 3.6 + - - -
136B GLU* 1.3 71.0 - - - +
138B ILE* 1.3 57.0 + - - +
145B MET* 3.2 6.6 - - - +
146B LEU* 2.6 36.1 + - + -
147B PHE* 2.8 55.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.1 3.3 - - - +
75B TYR* 2.8 65.2 + - + +
77B ASN* 3.3 26.5 - - - +
136B GLU* 4.0 16.2 - - + +
137B ALA* 1.3 81.4 - - - +
139B SER* 1.3 68.8 + - - +
143B GLU* 3.4 30.7 - - + +
144B GLU 3.0 19.5 - - - +
145B MET* 4.3 6.3 - - + +
146B LEU* 4.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ARG* 4.0 3.3 + - - +
70B ASP 2.9 14.6 + - - -
71B LEU* 3.6 9.0 - - - -
73B GLN* 4.0 9.6 - - - -
74B LEU* 3.4 25.1 - - - -
138B ILE* 1.3 84.3 - - - +
140B GLY* 1.3 70.7 + - - +
143B GLU* 3.1 3.4 - - - +
144B GLU* 3.1 29.8 + - - +
146B LEU* 3.7 17.8 - - - +
----------------------------------------------------------
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