Contacts of the strand formed by residues 160 - 168 (chain B) in PDB entry 5U2H
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 LYS 160 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE* 3.7 7.8 - - - +
129B CYS 2.7 46.3 + - - +
130B SER 5.0 3.1 - - - +
152B CYS* 3.9 12.6 - - + -
153B VAL 3.0 15.9 - - - +
154B VAL* 4.1 7.4 - - + +
158B ARG 4.0 2.5 + - - +
159B LEU* 1.3 74.9 - - - +
161B THR* 1.3 56.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PRO* 3.9 3.1 - - - +
121B ASP* 2.6 31.9 + - - +
123B PRO* 3.4 39.7 - - + -
127B THR* 3.2 24.2 - - - +
128B ILE* 3.9 4.3 - - + -
129B CYS* 3.4 6.7 - - - +
153B VAL* 2.6 38.6 + - - +
155B TYR* 3.8 10.7 - - - +
159B LEU* 3.7 1.6 + - + -
160B LYS* 1.3 76.6 - - - +
162B CYS* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASP* 3.2 21.4 + - + +
127B THR 3.8 5.0 + - - +
129B CYS* 3.4 9.3 - - + +
135B CYS* 2.0 53.6 - - + -
148B GLN* 3.7 14.6 - - + +
150B GLY 3.8 0.4 - - - -
151B ARG 3.3 19.1 - - - -
153B VAL* 4.1 1.6 - - - -
161B THR* 1.3 75.7 - - - +
163B GLU* 1.3 76.8 + - - +
164B VAL* 3.3 7.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.5 22.1 - - + +
119B CYS* 3.9 19.2 - - - +
120B PRO* 5.5 0.4 - - + -
148B GLN* 3.4 3.3 - - - -
149B THR* 2.7 55.9 + - - +
151B ARG* 2.7 61.8 + - - +
153B VAL* 3.6 25.4 - - + +
162B CYS* 1.3 69.8 - - - +
164B VAL* 1.3 56.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLY 4.0 0.3 - - - +
118B LEU* 3.3 3.4 - - - +
119B CYS* 2.9 47.3 + - - +
121B ASP* 3.7 19.1 - - + +
144B SER* 5.0 0.4 - - - +
146B GLY* 4.0 9.9 - - - -
147B ILE 3.1 14.8 - - - +
148B GLN* 4.0 23.8 - - + +
149B THR* 4.5 3.4 - - - -
162B CYS* 3.4 15.5 - - + +
163B GLU* 1.3 76.0 - - - +
165B SER* 1.3 62.2 + - - +
166B ALA 4.0 1.0 + - - +
170B ILE* 3.2 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLY* 3.4 13.0 + - - -
118B LEU* 4.3 3.8 - - - +
146B GLY* 4.0 0.2 - - - -
147B ILE* 2.7 37.1 + - - +
149B THR* 4.4 13.0 - - - -
164B VAL* 1.3 71.9 - - - +
166B ALA* 1.3 67.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
116B GLN* 3.5 4.7 - - - -
117B GLY 2.9 34.0 + - - +
145B LYS 3.5 25.4 - - - +
146B GLY* 3.9 5.8 - - - -
164B VAL* 4.0 6.0 + - + +
165B SER* 1.3 76.7 + - - +
167B TRP* 1.3 73.7 + - + +
168B CYS* 3.4 3.0 + - - -
170B ILE* 5.2 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLN* 3.5 34.8 - - + +
115B GLN* 3.7 8.3 - - - -
116B GLN* 3.4 43.7 - - + -
145B LYS 6.1 0.7 - - - -
166B ALA* 1.3 81.3 - - + +
168B CYS* 1.3 60.1 + - - +
169B PRO 3.4 1.1 - - - -
170B ILE* 3.3 30.0 + - - +
298B TYR* 4.6 10.3 - + - -
305B GLU* 5.6 9.6 - - + -
306B LYS 5.8 0.9 - - - -
307B ARG* 4.7 18.8 - - + -
309B LEU* 5.3 7.9 - - + -
404B 7S1 4.4 29.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLY 3.7 2.8 - - - +
114B GLN* 3.3 2.9 - - - -
115B GLN* 2.9 44.1 + - + +
117B GLY* 3.4 36.3 - - - -
118B LEU 3.4 2.9 - - - +
119B CYS* 2.0 48.7 - - + -
166B ALA 3.5 3.6 - - - -
167B TRP* 1.3 72.3 - - - +
169B PRO* 1.3 63.1 - - + +
----------------------------------------------------------
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