Contacts of the strand formed by residues 130 - 139 (chain K) in PDB entry 1UW9
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 LEU 130 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E ARG* 2.8 44.8 + - - +
42K MET* 5.3 0.2 - - + -
43K THR 3.7 11.2 - - - +
45K GLN* 3.9 3.0 + - - +
53K CYS* 3.9 17.0 - - - -
56K ALA* 6.4 0.9 - - + -
57K VAL* 3.9 25.8 - - + -
124K VAL 3.5 24.0 - - - +
125K PHE 3.9 5.6 - - - +
127K PHE* 3.1 14.9 - - + +
128K LYS 3.1 2.6 - - - +
129K ALA* 1.3 79.7 - - + +
131K ARG* 1.3 62.3 + - - +
132K ALA* 4.0 19.1 - - - +
133K LEU* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E ARG* 4.7 3.2 - - - +
304E GLN* 3.0 18.7 + - - +
470E ASP* 2.9 32.5 + - - +
472E ILE* 3.5 40.5 - - + +
43K THR* 2.7 24.1 + - + +
44K PRO 3.9 12.3 - - - +
45K GLN* 3.1 41.7 + - - +
46K PRO* 4.1 13.0 - - - +
95K ASN* 4.7 7.2 - - - +
130K LEU* 1.3 75.0 - - - +
132K ALA* 1.3 58.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E GLN* 3.8 9.0 - - - +
41K ARG 4.4 0.2 - - - -
42K MET* 3.9 0.5 - - - -
43K THR* 2.9 42.0 + - + +
130K LEU* 3.6 8.6 - - - +
131K ARG* 1.3 83.5 - - + +
133K LEU* 1.3 63.7 + - - +
306K ASN* 3.5 31.6 - - + +
307K HIS* 3.7 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K PHE* 3.8 32.3 - - + -
41K ARG 3.3 15.7 - - - +
42K MET* 3.9 17.9 - - + -
57K VAL* 4.3 13.7 - - + -
124K VAL* 3.7 39.5 - - + +
125K PHE* 3.2 36.1 - - + -
130K LEU* 4.0 15.7 - - + -
132K ALA* 1.3 75.9 - - - +
134K ARG* 1.3 62.2 + - - +
306K ASN 3.7 2.2 - - - -
307K HIS* 3.2 8.5 + - - -
308K GLY 2.9 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K PHE* 3.4 4.3 - - - -
41K ARG* 2.7 48.1 + - + +
125K PHE* 4.4 0.9 - - - -
133K LEU* 1.3 75.3 - - - +
135K LEU* 1.3 64.0 + - - +
136K GLU* 3.0 37.5 + - - -
302K ASP 3.0 24.2 + - - -
304K GLN 3.2 19.8 + - - -
305K ARG* 3.4 22.1 + - - +
306K ASN 3.8 12.6 - - - +
307K HIS 3.7 2.4 + - - -
308K GLY 3.1 26.7 - - - +
309K ILE 4.0 2.8 - - - +
310K HIS* 3.5 27.0 - - - +
473K ASP* 2.8 29.9 + - - -
474K LYS 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K ALA* 3.8 21.8 - - + -
39K ALA 3.7 9.2 - - - +
40K PHE* 4.0 15.0 - - + -
117K PHE* 5.8 1.8 - - + -
120K ILE* 4.1 4.5 - - + -
121K VAL* 3.7 22.7 - - + -
125K PHE* 4.0 16.5 - - + -
134K ARG* 1.3 70.9 - - - +
136K GLU* 1.3 58.7 + - - +
137K ASP 3.5 20.0 - - - +
138K LEU* 3.9 14.1 - - + -
308K GLY 2.9 11.4 + - - +
309K ILE* 3.4 10.1 - - + +
310K HIS 2.9 26.7 + - - -
313K VAL* 3.9 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K ALA* 2.8 14.2 + - + +
41K ARG* 2.8 55.9 + - + +
98K ILE* 4.9 0.9 - - + -
134K ARG* 3.0 32.4 + - - +
135K LEU* 1.3 74.5 - - - +
137K ASP* 1.3 62.0 + - - +
310K HIS* 3.8 5.0 - - - +
312K ARG* 2.8 55.2 + - - +
313K VAL* 3.6 3.8 - - - +
363K TYR* 3.7 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K ALA* 3.5 3.6 - - - -
39K ALA* 3.0 25.1 + - + -
135K LEU* 3.5 6.1 - - - +
136K GLU* 1.3 77.6 - - - +
138K LEU* 1.3 70.7 + - - +
312K ARG* 4.0 14.4 - - - +
313K VAL* 3.5 8.4 - - - +
316K LYS* 3.2 25.7 + - - +
348K LEU* 5.2 0.9 - - - +
362K ILE* 3.8 6.6 - - - +
363K TYR* 2.9 47.6 + - + -
364K PHE* 3.4 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K ILE* 4.6 2.2 - - + -
37K LEU 3.1 15.7 - - - +
38K ALA* 3.6 17.3 - - + -
116K MET* 3.7 36.3 - - + -
117K PHE* 4.9 2.9 - - + -
120K ILE* 3.8 21.1 - - + -
135K LEU* 3.9 19.1 - - + -
137K ASP* 1.3 84.1 + - - +
139K ARG* 1.3 56.1 + - - +
140K ILE* 3.6 13.6 + - + -
313K VAL* 3.8 23.5 - - + +
316K LYS* 2.6 40.5 + - + +
364K PHE* 3.7 4.7 - - - -
366K GLN* 3.5 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K VAL* 4.8 4.8 - - - +
32K ARG 3.0 23.6 + - - -
33K ASP* 4.0 20.7 + - - -
35K ASP 2.8 28.9 + - - -
36K ILE* 3.5 4.0 - - - +
37K LEU* 2.7 61.3 + - + +
138K LEU* 1.3 70.2 - - - +
140K ILE* 1.3 71.7 + - - +
141K PRO* 3.3 17.1 - - - +
142K PRO* 5.6 1.7 - - - +
364K PHE* 3.5 23.8 - - + -
365K THR 3.5 24.6 + - - +
366K GLN* 3.9 4.0 - - - +
367K ASP 6.0 0.7 - - - +
----------------------------------------------------------
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