Contacts of the strand formed by residues 127 - 131 (chain B) in PDB entry 3C3K
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 ILE 127 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL* 4.3 9.6 - - + -
119B LEU* 3.7 40.2 - - + -
120B VAL* 3.9 24.5 - - + -
124B LYS* 4.3 11.2 - - + +
125B LYS 3.8 1.4 + - - -
126B ARG* 1.3 76.4 - - - +
128B ALA* 1.3 63.9 + - - +
146B TYR* 2.7 37.1 + - + -
150B LEU* 3.9 23.5 - - + +
155B LEU* 4.4 2.7 - - + -
157B TYR* 3.4 13.7 + - - -
187B ALA* 3.4 21.1 - - + +
189B PHE* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ARG 3.8 0.4 + - - -
127B ILE* 1.3 75.4 - - - +
129B LEU* 1.3 60.3 + - - +
146B TYR* 3.5 2.7 - - - -
157B TYR* 3.8 20.2 - - - +
159B ARG 3.3 11.7 - - - +
178B LEU* 3.7 28.3 - - + -
185B PRO* 4.0 6.5 - - + -
187B ALA 2.8 13.5 + - - +
188B ILE* 4.3 2.2 - - + -
189B PHE* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ALA* 1.3 74.6 - - - +
130B ILE* 1.3 68.9 + - - +
131B ASN* 3.8 14.8 + - + +
142B ARG 4.8 1.1 - - - +
143B GLU* 3.7 38.6 - - + +
146B TYR* 3.8 31.4 + - + -
159B ARG 2.8 10.0 + - - +
160B ILE* 3.3 8.7 - - + -
161B SER* 2.8 27.0 + - - +
178B LEU* 4.6 1.6 - - - +
189B PHE* 3.2 34.8 - - + +
191B ILE* 3.4 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 1.3 75.5 - - - +
131B ASN* 1.3 65.5 + - - +
161B SER* 3.3 6.7 - - - +
163B ALA* 4.1 11.4 - - + -
171B GLY* 3.7 11.0 - - - +
174B ALA* 3.5 26.0 - - + -
175B THR* 3.4 26.7 - - - +
178B LEU* 4.1 9.9 - - + -
188B ILE* 3.8 23.8 - - + -
189B PHE 3.0 7.7 + - - +
190B ALA* 3.6 13.4 - - + -
191B ILE* 3.2 28.6 + - - +
195B LEU* 4.2 16.2 - - + +
199B ALA* 4.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.8 13.6 - - + +
130B ILE* 1.3 77.5 - - - +
132B HIS* 1.3 79.1 + - - +
134B LEU* 3.5 8.1 - - - +
139B ALA* 3.1 40.4 + - - +
143B GLU* 3.0 30.1 + - - +
160B ILE* 4.2 2.0 - - + -
161B SER 2.9 6.9 + - - -
162B TYR* 3.3 21.3 - - + -
163B ALA* 2.7 26.5 + - - +
191B ILE* 3.6 17.9 - - - +
195B LEU* 4.8 0.2 - - - -
----------------------------------------------------------
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