Contacts of the strand formed by residues 141 - 151 (chain P) in PDB entry 3KYM
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 141 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114O SER* 5.1 2.9 - - - +
116O PHE* 3.8 33.7 - - + -
139P GLU* 2.9 10.9 + - - +
140P SER* 1.3 83.6 + - - +
142P ALA* 1.3 67.1 + - - +
189P THR* 4.9 8.1 - - - -
190P VAL 3.7 12.1 + - - +
191P PRO* 4.6 4.9 - - - +
192P SER 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116O PHE* 5.0 0.7 - - - -
132P PRO* 5.7 5.8 - - + -
141P THR* 1.3 79.0 - - - +
143P ALA* 1.3 62.2 + - - +
144P LEU 4.3 0.2 + - - -
188P VAL 4.0 0.3 - - - +
189P THR* 3.3 2.7 - - - -
190P VAL* 2.7 44.0 + - - +
192P SER* 5.5 4.7 - - - +
195P PHE* 3.4 35.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116O PHE* 3.7 45.4 - - + -
118O PHE* 3.4 17.2 - - + -
135O LEU* 3.9 15.3 - - + -
132P PRO* 3.7 15.8 - - - +
142P ALA* 1.3 74.8 - - - +
144P LEU* 1.3 64.0 + - - +
188P VAL 3.6 5.6 - - - +
189P THR* 4.0 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O PHE* 3.8 6.3 - - - -
130P LEU 3.4 15.7 - - - +
132P PRO* 4.7 7.9 - - + -
142P ALA 5.7 0.2 - - - +
143P ALA* 1.3 76.5 - - - +
145P GLY* 1.3 59.8 - - - +
160P TRP* 3.9 21.1 - - + -
187P VAL* 3.1 8.2 - - - +
188P VAL* 2.9 42.1 + - + +
190P VAL* 6.2 1.1 - - + -
195P PHE* 4.7 19.7 - - + -
200P TYR* 4.1 38.4 - - + -
217P VAL* 4.6 19.7 - - + +
219P ARG* 5.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P LEU* 3.1 35.4 + - - +
144P LEU* 1.3 79.2 - - - +
146P CYS* 1.3 59.9 + - - -
160P TRP* 3.6 11.2 - - - -
186P SER 2.8 15.0 - - - -
187P VAL* 3.8 1.3 - - - -
217P VAL* 3.4 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 146 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P VAL* 3.8 13.2 - - + -
128P PHE 3.5 5.8 - - - -
130P LEU* 3.7 5.5 - - - +
145P GLY* 1.3 77.8 - - - -
147P LEU* 1.3 60.5 + - - +
148P VAL* 4.0 7.2 + - + +
158P VAL* 5.6 0.4 - - + -
160P TRP* 4.1 2.0 - - + -
184P LEU 4.0 0.2 - - - +
185P SER* 3.2 3.5 - - - -
186P SER* 2.7 35.9 + - - +
202P CYS* 2.0 54.3 - - + -
204P VAL* 5.3 0.2 - - + -
215P LYS* 3.9 5.4 - - - -
217P VAL* 3.8 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124O GLN* 4.5 7.6 - - - +
131O SER* 3.8 30.1 - - - +
133O VAL* 4.4 15.5 - - + -
178O THR* 5.3 7.6 - - + +
126P SER 3.3 1.4 - - - +
127P VAL* 3.2 7.8 - - - +
128P PHE* 2.8 51.4 + - + +
130P LEU* 4.1 14.3 - - + +
146P CYS* 1.3 72.5 - - - +
148P VAL* 1.3 68.0 + - - +
149P LYS* 3.6 23.1 + - + -
183P SER* 5.1 3.1 - - - -
184P LEU 3.8 12.6 - - - +
185P SER* 4.1 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P PRO* 4.0 12.8 - - + -
126P SER 3.3 5.2 - - - +
127P VAL* 4.9 1.8 - - + -
146P CYS* 4.2 11.7 - - + +
147P LEU* 1.3 75.7 - - - +
149P LYS* 1.3 60.5 + - - +
151P TYR* 3.6 25.4 - - + -
156P VAL* 4.4 6.1 - - + -
158P VAL* 4.6 4.7 - - + -
183P SER* 3.3 22.0 - - - -
184P LEU* 2.7 35.9 + - + +
186P SER 5.3 0.9 - - - +
204P VAL* 3.9 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124O GLN* 3.9 19.7 - - + +
129O THR* 4.1 17.3 - - + +
131O SER* 4.0 18.4 - - - +
178O THR* 6.4 0.2 - - - -
180O THR* 4.9 9.8 - - - +
125P PRO* 3.4 2.2 - - - +
126P SER* 2.7 39.5 + - - -
128P PHE* 4.1 21.5 - - + -
147P LEU* 3.6 19.2 - - + -
148P VAL* 1.3 74.3 - - - +
150P ASP* 1.3 86.4 + - - +
177P GLN* 3.5 22.2 - - - +
183P SER* 4.0 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 150 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123P LYS* 3.2 20.2 + - - +
124P GLY 2.9 18.5 - - - +
125P PRO* 3.2 0.5 - - - +
126P SER* 4.9 4.3 - - - +
149P LYS* 1.3 113.5 + - + +
151P TYR* 1.3 59.9 + - - +
177P GLN* 3.9 9.7 + - - +
179P SER* 4.6 5.5 + - - -
181P LEU* 3.8 27.0 - - + +
182P TYR 3.1 12.9 + - - -
183P SER* 4.2 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 151 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123P LYS* 3.4 13.5 - - - +
124P GLY 4.2 0.2 - - - -
125P PRO* 3.3 26.0 - - + -
148P VAL* 3.6 42.4 - - + -
150P ASP* 1.3 71.6 - - - +
152P PHE* 1.3 64.8 + - - +
153P PRO 3.8 11.0 - - - -
154P GLU* 4.0 23.5 + - + +
156P VAL* 4.1 16.8 + - + +
174P ALA* 3.2 26.7 - - - +
181P LEU* 4.0 4.1 - - - +
182P TYR* 3.1 54.7 + - + +
183P SER* 3.9 3.6 - - - -
184P LEU* 3.4 13.5 - - + +
206P HIS* 4.2 9.4 - + + -
----------------------------------------------------------
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