Contacts of the strand formed by residues 171 - 180 (chain B) in PDB entry 4XXD
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 TYR 171 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B THR* 6.5 0.2 - - + -
139B ASP* 3.0 23.7 + - - -
140B TYR* 2.7 45.1 + - + +
141B PHE* 3.6 36.8 - + - -
142B PRO* 5.6 0.2 - - + -
143B GLU* 4.0 37.0 - - + -
163B ALA* 3.8 20.6 - - + -
164B VAL 3.7 1.8 - - - -
165B LEU* 3.7 44.5 - - + +
166B GLN* 3.7 0.2 - - - -
170B LEU* 1.3 72.4 - - - +
172B SER* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLN* 5.9 0.2 - - - -
178A THR* 6.0 0.5 - - - +
136B LEU* 3.7 12.5 - - - +
137B VAL 3.2 10.7 + - - -
138B LYS* 3.4 20.7 - - - +
140B TYR* 3.9 2.2 - - - -
162B PRO 4.4 0.2 - - - +
163B ALA* 3.4 1.1 - - - -
164B VAL* 2.8 36.3 + - - +
166B GLN* 3.6 26.2 + - - -
171B TYR* 1.3 76.9 - - - +
173B LEU* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 6.5 0.2 - - - -
136B LEU* 3.7 6.4 - - - +
137B VAL* 2.8 54.1 + - + +
140B TYR* 3.2 23.8 - - - +
143B GLU* 5.2 2.0 - - - +
145B VAL* 3.8 20.2 - - + +
147B VAL* 4.6 2.9 - - + -
160B THR* 4.2 16.6 - - + -
161B PHE* 3.4 24.5 - - - +
162B PRO* 3.9 3.6 - - + +
163B ALA* 3.9 14.8 - - + +
172B SER* 1.3 76.3 + - - +
174B SER* 1.3 72.3 + - - +
175B SER 4.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 4.9 6.1 - - - -
176A SER* 3.1 25.5 + - - -
178A THR* 5.1 2.0 + - - -
119B LEU* 4.2 16.4 - - - -
135B CYS 3.4 10.5 - - - -
136B LEU* 4.6 9.9 - - - -
161B PHE* 3.0 42.0 + - - +
173B LEU* 1.3 79.8 - - - +
175B SER* 1.3 61.0 + - - +
176B VAL* 5.0 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLY* 3.2 2.8 - - - -
135B CYS* 2.9 35.4 + - - -
137B VAL* 5.8 0.9 - - - -
147B VAL* 3.8 24.8 - - - +
149B TRP* 3.2 23.0 + - - -
158B VAL* 4.2 1.6 - - - +
159B HIS 3.4 6.0 + - - -
160B THR* 2.7 29.1 + - - +
173B LEU* 4.5 1.1 - - - +
174B SER* 1.3 73.2 - - - +
176B VAL* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 4.9 4.7 - - + -
133A VAL* 5.8 2.9 - - + -
135A LEU* 3.7 46.0 - - + -
137A ASN* 5.0 0.9 - - - +
176A SER* 5.9 0.2 - - - +
119B LEU* 4.5 16.2 - - + -
133B LEU 3.4 11.7 - - - +
134B GLY* 4.0 0.7 - - - -
149B TRP* 4.7 1.8 - - - -
157B GLY 4.6 0.4 - - - -
158B VAL* 3.5 5.2 - - - +
159B HIS* 2.8 54.7 + - + +
161B PHE* 3.7 13.7 - - + -
174B SER* 5.0 3.4 - - - +
175B SER* 1.3 78.6 - - - +
177B VAL* 1.3 65.0 + - - +
178B THR* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA 3.8 1.4 - - - +
132B ALA* 3.8 1.5 - - - -
133B LEU* 2.8 61.4 + - + +
149B TRP* 4.0 24.2 - - + -
154B LEU* 3.7 22.0 - - + -
156B SER 3.8 13.0 - - - +
157B GLY 3.7 4.5 - - - +
158B VAL* 3.6 27.8 - - + -
176B VAL* 1.3 75.1 - - - +
178B THR* 1.3 70.0 + - - +
179B VAL* 3.9 6.4 + - + -
189B TYR* 5.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 5.3 3.1 - - + -
135A LEU* 5.3 3.6 - - + -
137A ASN* 3.5 33.2 + - + +
138A ASN* 5.5 1.7 + - - -
130B THR* 4.2 23.1 - - + -
131B ALA 3.4 5.2 - - - +
132B ALA* 4.6 12.3 - - + -
156B SER 4.3 7.3 - - - +
157B GLY* 3.4 22.1 + - - +
159B HIS* 5.6 1.0 + - + -
176B VAL* 6.2 1.3 - - + -
177B VAL* 1.3 78.1 - - - +
179B VAL* 1.3 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR* 3.7 2.9 - - - -
131B ALA* 2.7 42.0 + - + +
133B LEU* 3.8 17.3 - - + -
154B LEU* 4.4 10.5 - - + -
177B VAL* 4.3 15.9 - - + -
178B THR* 1.3 78.4 - - - +
180B PRO* 1.4 66.0 - - + +
184B LEU* 3.7 24.5 - - + -
189B TYR* 3.4 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLY 3.3 13.0 - - - +
130B THR* 4.6 1.3 - - - -
179B VAL* 1.4 88.9 - - + +
181B SER* 1.3 63.9 + - - +
182B SER* 3.9 13.5 - - - +
183B SER* 3.1 40.6 + - - +
184B LEU* 3.9 8.1 + - - +
189B TYR* 5.0 0.2 - - - +
----------------------------------------------------------
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