Contacts of the strand formed by residues 150 - 164 (chain B) in PDB entry 2YXD
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 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B GLU* 5.2 1.6 - - - -
148B GLY 3.7 1.8 + - - -
149B TYR* 1.3 75.3 - - - +
151B VAL* 1.3 64.2 + - - +
152B ASP* 4.2 2.4 + - - +
180B LYS 3.7 1.4 - - - +
181B ALA* 3.5 1.9 - - - -
182B VAL* 2.8 53.9 + - - +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ILE* 4.0 22.7 - - + +
144B PHE* 3.8 27.4 - - + -
145B GLU* 3.6 37.2 - - + +
149B TYR 4.0 2.2 - - - +
150B ASN* 1.3 83.0 + - - +
152B ASP* 1.3 64.3 + - - +
153B ALA* 4.2 2.5 + - + +
179B ILE* 3.7 28.5 - - + -
180B LYS 3.2 3.6 - - - +
181B ALA* 4.2 5.4 - - + -
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A TYR* 4.8 6.1 - - - +
30B LYS* 2.9 38.1 + - - +
150B ASN* 4.2 3.5 + - - +
151B VAL* 1.3 72.5 - - - +
153B ALA* 1.3 59.4 + - - +
154B VAL* 3.9 14.5 - - - +
178B ILE 3.9 1.0 - - - +
179B ILE* 3.7 0.3 - - - -
180B LYS* 2.8 55.9 + - + +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A TYR* 3.9 0.7 - - - +
161A ALA* 3.0 45.5 + - + +
170A PHE* 4.4 1.1 - - + -
141B ILE* 3.8 27.1 - - + -
151B VAL* 4.0 4.2 + - + -
152B ASP* 1.3 75.0 + - - +
154B VAL* 1.3 69.3 + - - +
177B THR* 4.6 4.7 - - + -
178B ILE 3.3 4.5 - - - -
179B ILE* 4.0 15.3 - - + +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLU* 3.8 11.7 - - + +
158A ILE* 4.0 8.1 - - + -
159A SER 3.4 9.0 - - - +
160A TYR* 3.5 31.6 - - + -
170A PHE* 3.9 5.2 - - - -
26B VAL* 4.7 4.5 - - + -
30B LYS* 4.4 12.3 - - - +
152B ASP* 3.9 10.1 - - - +
153B ALA* 1.3 80.7 - - - +
155B ASN* 1.3 60.6 + - - +
156B VAL* 3.9 21.1 - - + -
176B ILE 3.9 0.2 - - - +
177B THR* 3.4 4.0 - - - +
178B ILE* 2.8 50.9 + - + +
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Residues in contact with ASN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A PHE 3.7 1.6 - - - +
158A ILE* 3.3 5.5 - - - +
159A SER* 2.8 45.9 + - - +
170A PHE* 3.7 8.7 - - + -
154B VAL* 1.3 72.4 - - - +
156B VAL* 1.3 64.2 + - - +
157B PHE* 4.7 3.3 + - - +
175B PRO* 3.9 11.6 - - - +
176B ILE 3.5 6.3 + - - +
177B THR* 2.8 26.5 + - - +
2001B MES 3.1 58.1 + - - +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A VAL* 4.1 16.6 - - + -
157A PHE 3.7 2.0 - - - -
158A ILE* 4.4 14.6 - - + +
23B ILE* 3.4 29.0 - - + +
26B VAL* 4.9 9.4 - - + -
154B VAL* 3.9 22.2 - - + -
155B ASN* 1.3 78.9 - - - +
157B PHE* 1.3 60.1 + - - +
158B ILE* 3.7 18.4 + - + +
174B ASN 4.5 0.5 - - - +
175B PRO* 3.2 24.8 - - - +
176B ILE* 2.9 18.3 + - - +
178B ILE* 3.9 16.4 - - + -
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ASN* 3.7 6.6 - - - +
156A VAL* 3.6 4.3 - - - -
157A PHE* 2.8 66.0 + + + +
155B ASN* 4.2 3.1 - - - +
156B VAL* 1.3 74.4 - - - +
158B ILE* 1.3 65.3 + - - +
159B SER* 4.2 18.4 - - - -
172B ALA* 3.5 33.0 - - + -
173B LYS 3.7 13.7 - - - -
175B PRO* 4.4 17.5 - - + -
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Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 6.1 0.2 - - + -
154A VAL* 4.2 4.5 - - + -
155A ASN 3.5 9.4 - - - +
156A VAL* 4.6 9.4 - - + -
20B LYS* 4.6 7.2 - - - -
22B GLU* 3.2 31.4 - - + -
23B ILE* 3.6 27.1 - - + -
156B VAL* 3.7 16.0 + - + -
157B PHE* 1.3 84.1 - - - +
159B SER* 1.3 70.5 + - - +
160B TYR* 3.6 32.8 - - + +
172B ALA* 3.9 0.3 - - - -
173B LYS* 2.9 32.6 + - + +
174B ASN 5.3 1.6 + - - +
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A VAL* 3.1 5.9 - - - +
155A ASN* 2.6 56.4 + - - +
157B PHE* 4.2 16.0 - - - -
158B ILE* 1.3 76.3 - - - +
160B TYR* 1.3 62.3 + - - +
170B PHE* 4.0 16.1 - - - +
171B LEU 3.3 21.5 - - - -
172B ALA* 3.8 5.6 - - - -
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Residues in contact with TYR 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASP* 4.8 6.5 - - - -
153A ALA 3.5 3.8 - - - +
154A VAL* 3.0 35.2 - - + -
20B LYS* 2.7 28.5 - - + +
22B GLU* 2.6 31.1 + - - +
158B ILE* 3.6 11.3 - - + +
159B SER* 1.3 72.0 - - - +
161B ALA* 1.3 67.7 + - - +
162B LYS* 3.4 1.7 + - - +
170B PHE* 3.7 2.9 - - - -
171B LEU* 2.9 38.7 + - + +
173B LYS* 2.9 43.3 - - + -
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ILE* 4.3 9.6 - - + -
153A ALA* 2.9 34.0 + - + +
160B TYR* 1.3 74.6 - - - +
162B LYS* 1.3 60.3 + - - +
163B LYS 4.2 0.6 + - - -
168B HIS* 4.4 14.6 - - + -
169B MSE 3.2 8.3 - - - +
170B PHE* 3.5 24.9 - - + -
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ALA* 1.3 73.9 - - - +
163B LYS* 1.3 74.9 - - - +
164B ILE* 3.6 11.0 + - + +
168B HIS* 3.2 4.0 - - - -
169B MSE 2.6 43.4 + - + +
171B LEU* 3.9 41.0 - - + +
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLU* 3.3 40.8 + - - +
161B ALA 4.3 0.2 + - - -
162B LYS* 1.3 83.0 - - - +
164B ILE* 1.3 75.4 + - - +
167B GLY 3.4 13.9 - - - +
168B HIS* 3.5 17.4 - - + +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LYS* 4.1 15.7 - - + +
163B LYS* 1.3 90.3 - - - +
165B PRO* 1.3 70.7 - - + +
166B SER* 3.8 18.2 - - - +
167B GLY* 2.8 45.0 + - - +
168B HIS* 4.0 6.3 - - - +
169B MSE 3.9 37.5 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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