Contacts of the strand formed by residues 138 - 145 (chain C) in PDB entry 1K4R
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 VAL 138 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ALA 3.9 0.5 - - - +
48C ILE* 3.3 5.4 - - - +
49C TYR* 2.7 75.4 + - + +
50C GLN* 5.5 0.4 - - - -
51C GLU 6.1 0.2 - - - +
136C LYS 3.8 10.3 - - - +
137C ILE* 1.3 77.9 - - - +
139C TYR* 1.3 66.1 + - - +
140C THR* 4.1 2.7 - - - +
164C SER* 3.9 25.6 - - - +
165C PHE 3.4 9.2 - - - +
166C THR* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 3.9 10.1 - - + -
47C ALA 3.5 4.3 - - - -
48C ILE* 3.5 42.6 - - + +
137C ILE* 4.0 13.2 - - + +
138C VAL* 1.3 78.6 - - - +
140C THR* 1.3 61.1 + - - +
141C VAL* 5.4 0.4 - - + -
164C SER* 3.5 1.2 - - - -
165C PHE* 2.8 47.5 + - + +
186C CYS* 6.1 0.2 - - + -
188C VAL* 3.5 41.2 + - + +
191C GLY* 3.5 6.9 - - - -
192C VAL* 3.3 33.6 + - - +
194C LEU* 5.5 0.7 - - - +
283C LEU* 5.8 0.2 - - - +
287C HIS 3.7 16.4 - - - -
288C VAL* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 3.4 6.2 - - - +
46C ASP* 2.7 46.2 + - + +
47C ALA* 3.0 22.7 + - + -
49C TYR* 3.9 20.4 + - - -
138C VAL* 4.1 0.5 - - - +
139C TYR* 1.3 72.6 - - - +
141C VAL* 1.3 60.0 + - - +
142C LYS* 4.8 3.1 - - + +
162C THR* 3.4 30.5 - - + -
163C ALA 3.4 4.0 - - - +
164C SER* 3.5 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 4.0 13.7 - - + -
43C VAL* 3.8 24.2 - - + -
44C TRP 3.4 9.6 - - - +
45C LEU* 4.2 15.0 - - + -
139C TYR* 4.8 1.3 - - + +
140C THR* 1.3 77.9 - - - +
142C LYS* 1.3 65.1 + - - +
143C VAL* 5.1 1.0 - - - +
161C LYS 4.0 0.2 - - - +
162C THR* 3.5 2.9 - - - +
163C ALA* 2.8 40.3 + - - +
165C PHE* 3.8 28.9 - - + -
184C LEU* 4.1 17.9 - - + -
186C CYS* 4.1 10.3 - - - -
288C VAL* 4.9 2.9 - - + -
290C CYS* 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL* 3.3 6.8 - - - +
44C TRP* 2.9 68.5 + - + +
46C ASP* 3.2 37.2 - - + +
140C THR* 4.8 1.7 - - - +
141C VAL* 1.3 75.5 - - - +
143C VAL* 1.3 65.2 + - - +
160C ARG* 4.1 15.9 - - + +
161C LYS 3.3 4.7 - - - +
162C THR* 2.9 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C MET* 3.8 31.6 - - + -
42C ASP 3.3 8.5 - - - +
43C VAL* 4.3 19.3 - - + -
141C VAL 5.1 0.2 - - - +
142C LYS* 1.3 80.8 - - - +
144C GLU* 1.3 63.5 + - - +
160C ARG* 3.3 4.6 - - - +
161C LYS 2.8 32.9 + - - -
174C LEU* 3.9 16.8 - - + -
176C MET* 3.8 14.7 - - + +
182C VAL* 4.7 7.0 - - + -
184C LEU* 3.9 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER* 3.8 6.6 + - - -
2C ARG* 2.9 32.2 + - - +
41C MET* 3.6 4.2 - - - -
42C ASP* 2.8 40.3 + - + +
44C TRP* 4.0 13.0 - - + -
143C VAL* 1.3 77.5 - - - +
145C PRO* 1.3 78.5 - - + +
146C HIS* 4.4 0.6 - - + -
151C VAL* 6.0 0.3 - - - +
157C HIS* 3.5 32.6 - - + +
160C ARG* 2.7 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C SER* 6.1 0.3 - - - -
39C PRO* 5.9 0.9 - - + -
40C SER 4.5 0.4 - - - +
41C MET* 3.6 22.2 - - - -
144C GLU* 1.3 92.7 - - + +
146C HIS* 1.3 62.3 + - - +
147C THR* 3.3 23.8 + - + +
157C HIS* 3.7 13.2 + - + -
159C GLY* 3.2 30.7 - - - +
176C MET* 3.6 12.8 - - + +
179C TYR* 4.0 31.6 - - + -
----------------------------------------------------------
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