Contacts of the strand formed by residues 137 - 147 (chain A) in PDB entry 3IU3
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 THR 137 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A THR* 3.3 8.3 - - - +
134A SER* 2.9 38.5 + - - -
135A GLY 3.2 1.2 - - - -
136A GLY* 1.3 79.9 - - - +
138A ALA* 1.3 70.3 + - - +
185A THR* 3.6 25.6 - - + -
186A VAL 3.4 14.8 - - - +
187A PRO* 4.7 0.4 - - - -
188A SER* 3.5 3.6 - - - -
113B PHE* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PRO* 4.9 5.8 - - + -
132A SER 3.6 8.7 - - - +
133A THR* 4.2 9.4 - - - +
134A SER 4.9 0.2 - - - +
137A THR* 1.3 77.6 - - - +
139A ALA* 1.3 62.4 + - - +
185A THR* 3.4 2.4 - - - -
186A VAL* 2.8 39.0 + - + +
188A SER* 3.7 19.0 + - - +
191A LEU* 4.3 25.4 - - + -
113B PHE* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PRO* 4.0 6.0 - - - +
132A SER* 2.6 32.1 + - - -
138A ALA* 1.3 74.6 - - - +
140A LEU* 1.3 62.3 + - - +
183A VAL* 5.0 0.2 - - + -
184A VAL 3.6 4.9 - - - +
185A THR* 4.0 10.3 - - + +
113B PHE* 3.7 42.4 - - + -
115B PHE* 3.2 9.3 - - + -
132B LEU* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU 3.6 13.0 - - - +
128A PRO* 3.9 16.8 - - + -
138A ALA 6.0 0.2 - - - -
139A ALA* 1.3 75.8 - - - +
141A GLY* 1.3 59.7 + - - +
156A TRP* 3.6 30.3 - - + -
183A VAL* 3.4 4.7 - - - +
184A VAL* 2.8 47.7 + - + +
186A VAL* 4.2 11.2 - - + -
191A LEU* 4.0 21.3 - - + -
196A TYR* 3.8 37.0 - - + -
213A VAL* 4.1 11.2 - - + +
115B PHE* 4.1 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 2.7 46.0 + - - +
140A LEU* 1.3 79.6 - - - +
142A CYS* 1.3 59.4 + - - -
156A TRP* 3.5 14.8 - - - -
182A SER 3.0 12.6 - - - -
183A VAL* 4.1 1.1 - - - -
213A VAL* 3.7 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL* 4.1 12.8 - - + -
124A PHE 3.5 6.7 - - - +
125A PRO* 5.0 1.1 - - - -
126A LEU* 4.0 4.7 - - - +
141A GLY* 1.3 77.5 - - - -
143A LEU* 1.3 60.4 + - - +
144A VAL* 3.8 8.6 + - + +
156A TRP* 3.8 4.7 - - + -
181A SER* 3.3 4.3 - - - -
182A SER* 2.7 40.0 + - - +
198A CYS* 2.0 52.7 - - + -
200A VAL* 5.0 0.2 - - + -
211A LYS* 4.3 4.5 - - - -
213A VAL* 3.9 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER 3.4 2.3 - - - +
123A VAL* 3.3 5.0 - - - -
124A PHE* 2.7 57.8 + - + +
126A LEU* 4.1 13.8 - - + +
142A CYS* 1.3 71.6 - - - +
144A VAL* 1.3 60.3 + - - +
145A LYS* 4.4 12.1 - - + +
179A SER* 4.1 15.0 - - - +
180A LEU 3.7 11.0 - - - +
181A SER* 3.7 19.1 - - - +
121B GLN* 4.4 9.6 - - - +
128B SER* 3.6 34.3 - - - +
130B VAL* 4.6 12.3 - - + -
175B THR* 5.2 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO* 3.5 25.6 - - + -
122A SER 3.6 2.2 - - - -
123A VAL* 4.5 2.7 - - + +
142A CYS* 4.3 11.0 - - + +
143A LEU* 1.3 72.4 - - - +
145A LYS* 1.3 59.3 + - - +
147A TYR* 3.8 9.3 - - + -
152A VAL* 4.1 11.4 - - + -
154A VAL* 4.2 8.5 - - + -
179A SER* 3.2 5.0 + - - -
180A LEU* 2.9 55.7 + - + +
182A SER 5.2 0.4 - - - +
200A VAL* 3.8 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO* 3.4 2.5 - - - +
122A SER* 2.8 44.3 + - - +
124A PHE* 4.3 18.6 - - + -
143A LEU* 4.4 12.5 - - + +
144A VAL* 1.3 74.7 - - - +
146A ASP* 1.3 93.1 + - - +
147A TYR 3.7 1.3 - - - -
173A GLN* 3.1 20.0 + - - +
179A SER* 3.4 13.2 + - - +
121B GLN* 4.0 20.4 - - - +
126B THR* 4.7 10.5 - - - -
128B SER* 3.5 20.2 + - - +
175B THR* 5.8 0.4 - - - +
177B THR* 3.8 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS* 3.7 20.1 + - - +
120A GLY 3.5 14.6 - - - +
122A SER* 5.2 6.2 + - - +
145A LYS* 1.3 100.6 - - - +
147A TYR* 1.3 58.7 + - - +
173A GLN* 2.9 27.4 + - - -
175A SER* 4.6 0.7 + - - -
177A LEU* 3.7 26.4 - - + +
178A TYR 3.1 12.1 + - - -
179A SER* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS* 3.4 13.7 - - - +
121A PRO* 3.7 29.6 - - + -
144A VAL* 3.8 27.8 - - + -
146A ASP* 1.3 75.6 - - - +
148A PHE* 1.3 60.8 - - - +
149A PRO 3.4 21.8 - - - -
150A GLU* 3.0 27.0 + - - -
152A VAL* 3.8 19.2 - - + +
170A ALA* 3.3 14.9 - - - +
177A LEU* 3.5 3.7 - - - +
178A TYR* 2.6 80.3 + - + +
179A SER* 3.8 3.6 - - - -
180A LEU* 3.4 12.2 - - + +
202A HIS* 3.9 9.0 - + + -
----------------------------------------------------------
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