Contacts of the helix formed by residues 157 - 172 (chain B) in PDB entry 5SZK
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 ASN 157 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.3 25.9 - - + +
149B GLU* 2.9 25.7 + - - +
150B THR* 4.0 1.8 - - + -
155B ALA 3.1 3.6 + - - -
156B THR* 1.3 86.9 - - - +
158B VAL* 1.3 57.7 + - - +
159B GLU 3.3 2.9 - - - -
160B GLN* 3.1 18.7 + - - +
161B ALA* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.9 26.9 - - + +
27B ARG* 3.5 25.6 - - + -
28B PHE* 4.6 13.5 - - + +
150B THR* 4.0 8.5 - - - -
151B SER 3.6 18.6 - - - +
152B ALA* 4.2 4.7 - - - -
155B ALA* 3.6 11.3 + - + +
156B THR 3.2 14.3 - - - +
157B ASN* 1.3 78.4 - - - +
159B GLU* 1.3 67.1 + - + +
161B ALA* 3.5 2.7 + - - +
162B PHE* 3.0 37.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 4.1 20.4 - - + -
48B ARG* 3.6 28.3 + - - +
50B ILE* 3.8 9.4 - - - +
155B ALA 5.1 0.2 + - - -
157B ASN 3.3 0.4 - - - -
158B VAL* 1.3 82.5 - - + +
160B GLN* 1.3 61.4 + - - +
162B PHE* 3.2 2.3 + - - +
163B MET* 2.7 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.7 16.6 - - + -
157B ASN* 3.1 24.0 + - - +
159B GLU* 1.3 77.7 - - - +
161B ALA* 1.3 57.3 + - - +
163B MET* 3.1 12.0 + - - +
164B THR* 2.8 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 5.2 2.7 - - + -
117B LEU* 3.2 19.0 - - + +
119B VAL* 4.3 19.1 - - + -
148B LEU* 3.6 12.0 - - + +
150B THR* 4.1 17.5 - - + -
157B ASN 2.8 18.4 + - - +
158B VAL* 3.6 6.5 - - - +
159B GLU 3.2 0.2 - - - -
160B GLN* 1.3 73.4 - - - +
162B PHE* 1.3 60.9 + - + +
164B THR* 3.7 2.3 - - - -
165B MET 3.0 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.2 15.5 - - + +
13B LEU* 4.3 22.9 - - + -
24B LEU* 4.2 18.2 - - + -
25B LEU* 4.8 1.8 - - - -
28B PHE* 3.3 64.8 - + + -
59B LEU* 4.8 5.8 - - + +
61B ILE* 4.0 24.2 - - + -
85B ILE* 3.8 23.3 - - + -
158B VAL* 3.0 26.4 + - + +
159B GLU 3.2 2.2 + - - +
161B ALA* 1.3 81.7 - - + +
163B MET* 1.3 57.2 + - - +
165B MET* 3.3 6.2 + - - +
166B ALA* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 5.5 0.9 - - - -
50B ILE* 3.3 52.3 - - + -
51B GLU 4.1 6.7 - - - +
52B LEU* 3.5 33.8 - - + +
159B GLU* 2.7 47.6 + - + +
160B GLN* 3.6 13.5 - - - +
162B PHE* 1.3 69.8 - - - +
164B THR* 1.3 60.6 + - - +
166B ALA* 3.1 6.7 + - + +
167B ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 4.9 5.4 - - + -
146B PRO* 4.1 30.7 - - + -
148B LEU* 5.0 3.9 - - - +
160B GLN* 2.8 38.4 + - - +
161B ALA* 3.7 6.1 - - - -
163B MET* 1.3 73.2 - - - +
165B MET* 1.3 62.2 + - - +
167B ALA* 3.2 8.2 + - + +
168B GLU* 3.2 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.1 26.0 - - + -
83B GLY* 3.2 32.1 - - - -
84B ILE 4.4 1.6 - - - -
85B ILE* 4.1 16.4 - - + -
115B ASN* 3.3 32.5 - - + +
116B LYS 4.5 1.1 - - - -
117B LEU* 3.7 33.8 - - + +
161B ALA 3.0 15.3 + - - +
162B PHE* 3.4 12.6 - - - +
163B MET 3.2 0.2 - - - -
164B THR* 1.3 77.0 - - - +
166B ALA* 1.3 61.4 + - - +
168B GLU* 3.6 4.8 + - + +
169B ILE* 3.1 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.9 13.5 - - + -
11B LEU* 5.6 1.1 - - - +
50B ILE* 5.4 0.4 - - + -
52B LEU* 4.4 10.8 - - + -
57B ILE* 4.4 23.8 - - + -
59B LEU* 4.5 10.8 - - + -
162B PHE 3.0 13.3 + - - +
163B MET* 3.1 13.9 + - + +
165B MET* 1.3 74.4 - - - +
167B ALA* 1.3 66.5 + - - +
169B ILE* 3.1 6.3 + - - +
170B LYS* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.9 23.0 - - + +
163B MET 2.9 15.6 + - - +
164B THR* 3.5 13.9 - - + +
166B ALA* 1.3 72.2 - - - +
168B GLU* 1.3 57.8 + - + +
170B LYS* 2.9 19.8 + - - +
171B LYS* 3.0 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN* 3.4 29.8 + - + +
116B LYS 5.8 0.4 - - - -
144B GLY 5.1 3.8 - - - +
146B PRO* 3.4 37.8 - - + +
164B THR* 3.2 23.3 + - + +
165B MET* 4.1 5.4 - - + +
166B ALA 3.2 0.6 - - - -
167B ALA* 1.3 74.2 - - + +
169B ILE* 1.3 65.3 + - - +
171B LYS* 3.7 25.5 + - + +
172B ARG* 3.5 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 4.0 30.6 - - + -
11B LEU* 3.7 26.7 - - + -
82B HIS* 3.7 43.3 - - + +
83B GLY* 3.8 4.0 - - - +
115B ASN* 3.6 11.0 - - - +
165B MET* 3.1 27.5 + - + +
166B ALA* 3.1 6.6 + - - +
168B GLU* 1.3 78.6 - - - +
170B LYS* 1.3 57.5 + - - +
172B ARG* 3.0 31.1 + - - +
173B MET* 4.1 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 4.5 24.7 - - + +
9B PHE* 4.3 15.9 - - + -
52B LEU* 4.5 17.0 - - + -
53B ASP* 6.1 1.3 - - - +
55B LYS* 5.8 3.8 - - + +
57B ILE* 6.2 0.7 - - + -
166B ALA 3.0 9.8 + - - +
167B ALA 2.9 11.2 + - - +
169B ILE* 1.3 76.1 - - - +
171B LYS* 1.3 69.8 + - + +
172B ARG 2.6 17.5 - - - +
173B MET 4.2 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA* 3.0 35.8 + - - +
168B GLU* 3.8 32.5 - - + +
170B LYS* 1.3 88.9 + - + +
172B ARG* 1.3 62.2 + - - +
173B MET 4.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B HIS* 2.9 46.3 + - - +
113B ASN* 3.3 57.7 + - - +
114B VAL* 4.2 2.4 - - - +
115B ASN* 2.8 22.6 + - - +
168B GLU 3.5 8.3 + - - +
169B ILE* 3.0 17.4 + - - +
170B LYS* 2.6 22.9 - - - +
171B LYS* 1.3 79.4 - - - +
173B MET* 1.3 100.9 + - + +
----------------------------------------------------------
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