Contacts of the strand formed by residues 131 - 139 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1206A E55 4.6 18.2 - - + -
54D LEU* 3.6 30.1 - - + -
80D ILE* 6.0 1.8 - - + -
81D THR 3.7 2.2 - - - +
82D VAL* 3.4 47.5 - - + +
124D ILE* 3.7 24.5 - - + +
127D SER* 2.5 42.8 + - - -
128D LYS 5.1 0.4 - - - -
129D GLY 3.9 14.4 - - - -
130D LYS* 1.3 73.2 - - - +
132D LYS* 1.3 60.6 + - - +
133D CYS* 5.7 0.7 - - + -
151D PHE 3.4 1.2 - - - +
152D VAL* 3.3 4.1 - - - -
153D ILE* 2.7 67.9 + - + +
155D HIS* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D TYR 3.4 2.4 - - - +
80D ILE* 3.4 2.3 - - - +
81D THR* 2.7 57.1 + - + +
130D LYS* 4.0 8.6 + - + +
131D TYR* 1.3 73.8 - - - +
133D CYS* 1.3 62.7 + - - +
134D VAL* 5.0 11.2 - - + -
150D GLU* 4.7 20.4 - - + +
151D PHE 3.3 6.1 - - - +
152D VAL* 4.3 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1206A E55 3.9 31.6 - - + -
78D LEU* 4.4 4.5 - - - -
79D TYR 3.3 2.9 - - - -
80D ILE* 3.9 33.0 - - + -
131D TYR* 4.1 0.6 - - + -
132D LYS* 1.3 75.2 - - - +
134D VAL* 1.3 71.8 + - - +
135D VAL* 3.8 14.0 + - - +
149D LEU 3.5 1.7 - - - +
151D PHE* 2.7 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D CYS* 4.2 0.7 - - + -
77D ASN 3.6 0.2 - - - +
78D LEU* 3.6 2.8 - - - -
79D TYR* 3.0 64.6 + - + +
132D LYS* 5.0 9.9 - - + -
133D CYS* 1.3 77.6 - - - +
135D VAL* 1.3 68.2 + - - +
136D GLU* 4.0 1.8 - - + +
148D CYS* 3.5 28.0 - - - -
149D LEU 3.3 4.9 - - - +
150D GLU* 3.7 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1206A E55 4.3 33.2 - - + -
76D PHE* 4.9 6.7 - - + -
77D ASN 3.8 4.0 - - - -
78D LEU* 3.8 19.5 - - + -
133D CYS* 3.8 18.6 - - - +
134D VAL* 1.3 81.7 - - - +
136D GLU* 1.3 63.0 + - - +
137D ALA 3.4 3.8 + - - -
147D PHE* 3.8 13.6 - - + -
148D CYS* 3.6 1.6 - - - -
149D LEU* 3.0 42.4 + - + +
151D PHE* 4.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D TYR 3.6 1.9 - - - +
76D PHE* 3.5 3.9 - - - -
77D ASN* 3.2 49.6 + - + +
79D TYR* 3.4 29.9 + - + -
89D LYS* 4.3 1.2 + - - -
134D VAL* 4.0 0.8 - - - +
135D VAL* 1.3 71.9 - - - +
137D ALA* 1.3 61.9 + - - +
138D ILE* 4.0 10.8 - - + +
145D MET* 4.2 27.5 - - + +
147D PHE 3.6 10.1 - - - +
148D CYS* 4.2 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D LEU* 4.6 4.5 - - + -
75D TYR 3.9 4.3 - - - -
76D PHE* 4.0 16.2 - - + -
135D VAL 3.4 3.2 + - - -
136D GLU* 1.3 70.9 - - - +
138D ILE* 1.3 57.0 + - - +
145D MET* 3.2 6.9 - - - +
146D LEU* 2.6 35.2 + - + -
147D PHE* 2.8 55.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D LEU* 3.1 3.8 - - - +
75D TYR* 2.7 65.2 + - + +
77D ASN* 3.3 30.1 - - - +
136D GLU* 4.0 16.4 - - + +
137D ALA* 1.3 81.2 - - - +
139D SER* 1.3 67.9 + - - +
143D GLU* 3.4 31.6 - - + +
144D GLU 3.1 19.5 - - - +
145D MET* 4.3 5.8 - - + -
146D LEU* 4.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ARG* 4.1 3.3 + - - +
70D ASP 2.9 14.5 + - - -
71D LEU* 3.6 7.5 - - - -
73D GLN* 3.9 9.9 - - - -
74D LEU* 3.4 26.0 - - - -
138D ILE* 1.3 84.2 - - - +
140D GLY* 1.3 71.9 + - - +
143D GLU* 3.1 3.9 - - - +
144D GLU* 3.1 29.5 + - - +
146D LEU* 3.8 18.1 - - - +
----------------------------------------------------------
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