Contacts of the strand formed by residues 134 - 143 (chain F) in PDB entry 3SKU
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 ARG 134 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F VAL* 2.6 58.7 + - - +
33F VAL* 3.3 11.7 - - + +
53F PHE* 3.7 34.2 - - + -
54F ALA* 3.6 26.7 - - - +
125F GLU* 3.2 10.5 - - - +
126F PHE* 3.0 30.0 + - + +
132F GLY* 2.7 21.6 + - - +
133F ASN* 1.3 73.9 - - - +
135F GLU* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F VAL* 5.7 0.7 - - - +
33F VAL* 3.3 13.8 + - - +
68F GLN* 5.1 2.6 - - - +
75F LYS* 5.1 7.9 + - - -
123F ILE* 2.9 34.6 - - - +
124F CYS 3.0 18.6 - - - +
125F GLU* 3.9 19.1 - - + +
134F ARG* 1.3 79.7 - - - +
136F SER* 1.3 66.4 + - - +
137F GLN* 4.5 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F VAL* 5.0 7.0 - - - -
33F VAL* 2.6 33.0 + - - +
35F VAL* 3.3 15.8 - - - +
36F ASN 5.9 0.2 - - - -
123F ILE* 3.8 4.5 - - - +
124F CYS* 3.3 25.0 + - - +
135F GLU* 1.3 77.2 - - - +
137F GLN* 1.3 71.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F VAL* 4.7 6.0 - - - +
36F ASN 2.8 22.3 - - - +
37F ASP* 4.1 8.0 - - - +
70F SER* 5.3 1.2 - - - -
121F VAL* 3.1 27.9 - - + +
122F TYR 3.2 12.6 - - - +
123F ILE* 3.1 33.3 - - + +
124F CYS 5.1 0.4 - - - +
135F GLU* 4.5 8.2 + - - +
136F SER* 1.3 83.7 - - - +
138F LEU* 1.3 58.2 + - - +
1L NAG 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F VAL* 3.4 26.5 - - + -
36F ASN* 3.4 32.5 - - + +
37F ASP 3.5 8.7 - - - -
38F SER* 4.0 2.5 - - - +
39F MET* 4.7 1.8 - - + +
49F LEU* 3.2 44.0 - - + -
50F HIS 4.6 0.7 - - - +
67F TRP* 4.6 5.4 - - + -
121F VAL* 3.6 4.2 - - - -
122F TYR* 2.8 48.8 + - + +
137F GLN* 1.3 74.7 - - - +
139F ASN* 1.3 66.5 + - - +
140F LEU* 4.8 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 139 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ASP 3.0 14.0 + - - +
38F SER* 4.7 4.3 - - - -
39F MET* 2.9 34.5 + - - +
120F GLY* 3.6 18.2 - - - +
121F VAL* 3.8 5.2 - - - +
138F LEU* 1.3 73.7 - - - +
140F LEU* 1.3 61.4 + - - +
141F THR* 3.9 4.3 - - - +
1L NAG 1.4 74.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F MET* 3.4 31.0 - - + +
40F TYR* 4.8 1.6 - - - +
41F GLY 5.0 3.8 - - - +
47F VAL* 5.2 10.8 - - + -
49F LEU* 4.8 13.5 - - + -
111F LEU* 5.0 2.7 - - + -
114F LEU* 4.1 18.2 - - + -
118F ASP* 2.8 40.2 - - + +
119F GLU* 3.2 5.2 - - - +
120F GLY* 2.5 43.5 + - - +
122F TYR* 3.8 21.1 - - + -
138F LEU* 3.8 1.9 + - + -
139F ASN* 1.3 72.2 - - - +
141F THR* 1.3 67.3 + - - +
142F VAL* 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E HIS* 6.1 1.1 - - - +
39F MET 3.3 6.3 + - - +
40F TYR* 3.3 44.2 - - + +
41F GLY 3.5 4.3 + - - -
119F GLU* 3.0 23.5 + - - +
139F ASN* 3.9 5.3 - - - +
140F LEU* 1.3 76.0 + - - +
142F VAL* 1.3 66.4 + - - +
143F MET* 4.4 10.3 - - + -
178F LYS* 3.5 12.1 - - - +
179F PRO* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F GLY 3.6 15.7 - - - +
42F PHE 4.3 0.7 - - - -
43F ILE* 3.3 28.3 - - + +
114F LEU* 4.3 9.0 - - + -
115F GLU 2.8 31.4 - - - +
116F LEU* 3.3 22.0 - - + +
118F ASP* 4.1 6.5 - - + -
119F GLU* 3.4 16.7 - - + +
140F LEU* 4.2 9.6 - - + -
141F THR* 1.3 72.7 - - - +
143F MET* 1.3 60.1 + - - +
144F ALA 4.1 0.2 - - - -
178F LYS* 2.8 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E TYR* 5.3 2.2 - - + -
231E HIS* 4.3 14.4 - - - -
40F TYR* 3.9 31.4 - - + -
41F GLY 3.8 6.5 + - - +
42F PHE* 3.1 62.8 - - + -
43F ILE 3.3 3.5 + - - -
141F THR* 4.2 15.7 - - + +
142F VAL* 1.3 79.8 - - - +
144F ALA* 1.3 60.0 + - - +
178F LYS 3.1 7.6 - - - +
179F PRO* 4.4 7.4 - - + -
230F TYR* 3.3 20.2 - - + +
231F HIS* 3.8 27.1 - - + +
----------------------------------------------------------
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