Contacts of the strand formed by residues 168 - 176 (chain B) in PDB entry 4Y14
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 168 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLU* 3.6 31.6 + - - +
160B LEU 3.4 6.1 - - - -
161B GLU* 3.7 28.9 - - + +
166B GLN 3.6 6.0 + - - +
167B GLU* 1.3 82.6 - - - +
169B ARG* 1.3 70.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL 4.4 0.6 + - - -
100B TRP* 2.7 75.0 + - + +
103B LYS* 3.8 30.1 - - - +
104B SER 5.3 0.8 + - - -
105B ARG* 3.6 42.1 - - - +
159B GLU* 3.5 6.7 - - - -
160B LEU* 2.9 35.5 + - + +
167B GLU* 3.2 25.7 + - - +
168B THR* 1.3 79.8 - - - +
170B GLU* 1.3 62.2 + - - +
171B ILE* 3.7 11.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 3.6 20.0 - - - +
157B GLN* 2.7 41.1 + - + +
158B LEU 3.4 11.0 - - - +
159B GLU* 4.8 1.1 - - - +
169B ARG* 1.3 73.4 - - - +
171B ILE* 1.3 67.6 + - - +
172B LEU* 3.5 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TRP* 4.1 14.6 - - + -
99B VAL* 4.0 11.9 - - + -
104B SER 3.4 25.8 - - - +
105B ARG* 3.5 14.6 - - - +
106B GLY 4.4 0.2 - - - +
107B VAL* 4.1 22.2 - - + -
156B ARG 3.7 0.3 - - - +
158B LEU* 2.9 46.4 + - + +
160B LEU* 3.9 32.3 - - + -
169B ARG* 4.5 8.5 - - + -
170B GLU* 1.3 81.5 - - - +
172B LEU* 1.3 75.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG 2.9 9.8 + - - +
106B GLY* 3.4 2.4 - - - -
107B VAL 2.9 26.9 + - - +
155B VAL* 5.0 7.9 - - + -
156B ARG 3.5 11.4 - - - +
157B GLN* 4.1 12.8 - - + -
170B GLU* 3.5 27.4 - - + +
171B ILE* 1.3 78.8 - - - +
173B HIS* 1.3 59.3 + - - +
174B PHE* 3.6 21.4 - - + -
201B SER* 3.9 28.3 - - - +
203B SER* 3.7 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TRP* 5.4 0.2 - + - -
107B VAL* 3.5 24.0 - - + -
109B MET* 3.8 23.6 - - + +
124B TYR* 2.7 36.1 + + - -
125B TRP* 4.0 13.6 - + - -
154B THR 3.4 2.6 - - - +
155B VAL* 3.3 5.5 - - - +
156B ARG* 2.8 81.8 + - + +
158B LEU* 4.0 20.9 - - + -
171B ILE 3.8 0.2 + - - -
172B LEU* 1.3 73.3 - - - +
174B PHE* 1.3 62.1 + - - +
175B HIS* 4.0 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLY* 4.6 2.0 - - - -
107B VAL 2.8 20.3 + - - +
108B VAL* 3.5 10.9 - - + -
109B MET* 2.8 28.9 + - - +
154B THR 3.8 3.1 - - - -
155B VAL* 3.8 32.3 - - + -
172B LEU* 3.6 26.7 - - + -
173B HIS* 1.3 69.4 - - - +
175B HIS* 1.3 59.5 + - - +
194B PHE* 3.6 24.5 - + + -
197B LYS* 4.1 7.9 - - + -
198B VAL* 3.7 33.2 - - + -
201B SER* 3.3 35.2 - - - -
203B SER* 3.6 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B MET* 3.4 28.7 - - + -
111B ASN 2.6 29.7 + - - -
112B ARG* 4.3 0.4 - - - -
125B TRP* 4.0 6.6 - + - -
153B TYR* 3.2 6.6 - - - -
154B THR* 2.9 35.9 + - - +
156B ARG* 3.3 38.2 + - - +
173B HIS* 4.0 4.7 - - + -
174B PHE* 1.3 72.5 - - - +
176B TYR* 1.3 65.5 + - - +
177B THR* 3.5 21.6 + - + +
194B PHE* 4.0 3.5 - - - -
402B CL 3.5 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B MET 2.7 7.1 + - - -
110B LEU* 3.6 43.2 - - + +
111B ASN 3.8 1.7 - - - +
152B TYR* 3.6 24.4 - + - -
153B TYR* 4.3 0.4 - - - -
174B PHE 3.8 1.6 + - - -
175B HIS* 1.3 74.6 - - - +
177B THR* 1.3 63.7 + - - +
178B THR* 3.3 21.1 - - - -
179B TRP* 3.6 38.6 - + + -
185B PRO* 3.4 19.7 - - + +
186B GLU* 2.6 21.9 + - - -
190B SER* 3.6 15.5 - - - -
191B PHE* 4.3 8.5 - + + -
194B PHE* 3.5 40.1 - + + -
----------------------------------------------------------
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