Contacts of the strand formed by residues 177 - 185 (chain B) in PDB entry 6B0Z
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 GLY 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B VAL* 3.5 6.6 - - - +
146B VAL* 2.5 42.2 + - - +
172B PHE* 4.0 2.0 - - - -
176B GLY* 1.3 73.9 - - - -
178B VAL* 1.3 66.3 + - - +
184D ASN 3.4 10.8 - - - -
185D GLN 4.4 0.2 - - - -
186D ASP* 3.2 22.3 + - - -
222D ARG* 3.9 1.1 + - - +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE 3.4 11.9 - - - +
145B VAL* 4.2 5.2 - - + -
146B VAL* 4.1 4.5 - - - +
172B PHE* 3.9 3.1 - - - -
177B GLY* 1.3 80.0 - - - +
179B ALA* 1.3 63.3 + - - +
183D TYR* 3.3 4.0 - - - +
184D ASN* 2.9 47.9 + - + +
189D ILE* 4.7 4.0 - - + -
218D LYS 3.5 24.7 - - - +
219D TYR* 3.7 41.1 - - + +
222D ARG* 3.6 18.4 - - + -
223D PHE* 4.6 3.8 - - + -
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP* 3.5 0.2 - - - -
144B PHE* 3.0 58.3 + - + +
146B VAL* 4.1 7.4 - - + +
152B VAL* 4.0 19.7 - - + -
172B PHE* 5.1 0.2 - - + -
178B VAL* 1.3 77.3 - - - +
180B MET* 1.3 64.1 + - - +
182D MET 3.1 13.7 - - - +
183D TYR* 4.4 4.7 - - + -
219D TYR* 3.8 5.8 - - - -
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Residues in contact with MET 180 (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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138B GLN* 5.7 0.4 - - + -
141B ALA* 4.3 11.4 - - - -
142B THR 3.1 15.0 - - - +
143B ASP* 3.6 9.4 - - + -
144B PHE* 4.4 0.4 - - - -
179B ALA* 1.3 77.4 - - - +
181B GLY* 1.3 60.3 + - - +
182B MET* 4.6 4.5 - - - +
154D ILE* 3.6 10.4 - - - +
181D GLY* 3.2 4.9 - - - -
182D MET* 2.9 67.9 + - + +
216D LEU* 3.8 35.0 - - + -
219D TYR* 3.5 43.1 - - + -
270D LYS* 4.5 3.6 - - - +
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Residues in contact with GLY 181 (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 ALA* 3.4 4.7 - - - +
142B THR* 2.9 35.2 + - - -
154B ILE* 4.9 1.1 - - - -
180B MET* 1.3 74.0 - - - +
182B MET* 1.3 64.0 + - - +
154D ILE* 4.0 7.2 - - - +
169D VAL* 4.1 25.2 - - - +
180D MET 3.2 9.9 - - - -
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Residues in contact with MET 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASP* 3.7 20.9 - - - +
138B GLN* 3.7 33.7 - - - -
141B ALA* 3.5 18.2 - - + +
180B MET* 4.6 7.4 - - - +
181B GLY* 1.3 79.3 - - - +
183B TYR* 1.3 65.0 + - - +
216B LEU* 6.1 0.2 - - + -
219B TYR* 4.2 7.2 - - + +
270B LYS* 6.0 0.9 - - - +
169D VAL* 4.0 6.3 - - - +
179D ALA* 3.2 4.9 - - - +
180D MET* 2.9 62.2 + - + +
182D MET* 3.6 22.9 - - + -
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Residues in contact with TYR 183 (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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137B ASP* 3.7 12.6 + - - +
140B ARG* 3.5 53.3 + - + +
182B MET* 1.3 77.6 - - - +
184B ASN* 1.3 72.9 + - - +
185B GLN* 3.9 15.7 + - - -
219B TYR* 3.1 12.1 + - - -
169D VAL* 3.7 27.1 - - + -
170D HIS* 3.3 56.0 + + + -
172D PHE* 4.1 6.7 - + + -
178D VAL 3.2 12.1 - - - +
179D ALA* 4.1 2.2 - - + +
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Residues in contact with ASN 184 (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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133B HIS* 5.5 2.1 - - - +
137B ASP* 2.5 31.3 + - - +
183B TYR* 1.3 77.8 + - - +
185B GLN* 1.3 70.0 + - - +
188B SER* 3.8 17.5 + - - -
189B ILE* 4.4 4.1 - - + +
219B TYR* 3.6 6.9 + - + +
223B PHE* 3.6 27.5 - - + -
172D PHE* 3.6 3.9 - - - -
177D GLY* 3.2 2.6 - - - -
178D VAL* 2.8 45.1 + - + +
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Residues in contact with GLN 185 (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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183B TYR* 3.9 18.7 + - + -
184B ASN* 1.3 81.1 + - - +
186B ASP* 1.3 66.6 + - - +
187B LYS* 4.2 7.9 - - + +
188B SER* 3.0 32.0 + - - +
189B ILE* 3.1 15.5 + - - +
170D HIS* 3.7 27.6 + - + +
172D PHE* 4.1 12.2 - - + -
176D GLY 3.6 6.7 - - - +
177D GLY* 4.2 0.2 - - - -
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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