Contacts of the strand formed by residues 180 - 190 (chain B) in PDB entry 6JBQ
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 VAL 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B LEU* 3.4 38.8 - - + +
48B LEU* 4.3 12.0 - - + +
51B MET* 4.8 8.1 - - + -
178B SER* 3.7 17.5 - - - +
179B PRO* 1.3 89.2 - - + +
181B GLU* 1.3 61.2 + - - +
183B ILE* 3.8 27.4 - - + -
205B MET* 5.2 10.1 - - + -
206B GLU 3.6 4.5 - - - +
207B THR* 4.2 12.1 - - - +
211B ILE* 5.1 5.8 - - + -
216B ALA* 5.8 1.8 - - + -
821C ARG* 4.9 6.1 + - - -
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Residues in contact with GLU 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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48B LEU* 4.8 10.9 - - - +
179B PRO 5.1 1.6 - - - +
180B VAL* 1.3 76.6 - - - +
182B ARG* 1.3 59.5 + - + +
206B GLU* 2.7 30.7 + - + +
207B THR* 5.3 3.6 - - - +
821C ARG* 4.7 21.4 + - - +
1082C ILE* 5.4 2.6 - - - +
1093C PRO* 5.3 6.6 - - - +
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Residues in contact with ARG 182 (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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23B HIS* 3.9 4.6 + - - -
48B LEU* 5.4 1.1 - - - -
181B GLU* 1.3 85.2 - - + +
183B ILE* 1.3 61.3 + - - +
184B ALA* 4.6 2.2 - - - +
204B GLU* 3.5 29.7 + - - +
205B MET* 3.5 2.6 - - - -
206B GLU* 2.7 69.0 + - + +
1090C ASN* 2.9 34.5 + - - +
1091C GLY* 3.4 23.3 - - - +
1092C THR* 3.8 27.8 - - - +
1093C PRO* 5.6 2.2 - - + -
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Residues in contact with ILE 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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44B ARG* 3.5 48.2 + - + +
47B LEU* 4.6 19.5 - - + -
48B LEU* 3.8 30.1 - - + +
180B VAL* 3.8 27.6 - - + -
182B ARG* 1.3 80.8 - - - +
184B ALA* 1.3 64.8 + - - +
185B TYR* 5.9 0.4 - - + -
203B ILE* 4.4 17.9 - - + -
204B GLU 3.5 6.1 - - - +
205B MET* 3.8 18.6 - - + -
206B GLU 4.6 0.2 - - - +
1087C TYR* 5.1 0.3 - - - -
1091C GLY* 3.8 16.4 + - - +
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Residues in contact with ALA 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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44B ARG* 5.4 0.2 - - - +
182B ARG* 4.6 6.1 - - - +
183B ILE* 1.3 76.2 - - - +
185B TYR* 1.3 63.9 + - - +
203B ILE* 3.6 1.9 - - - +
204B GLU* 2.6 59.3 + - + +
1087C TYR* 5.8 2.5 - - - -
1089C GLU 4.8 5.4 - - - +
1090C ASN 3.4 27.4 - - - +
1091C GLY* 4.0 5.4 - - - -
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Residues in contact with TYR 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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36B GLY 4.7 3.6 - - - -
37B HIS* 4.3 20.7 + + - -
40B GLY* 3.8 12.3 - - - +
41B ASN* 3.3 40.0 - - - +
44B ARG* 4.0 22.7 - - + -
183B ILE* 5.9 0.9 - - + -
184B ALA* 1.3 79.3 - - - +
186B ASN* 1.3 70.9 + - - +
187B VAL* 5.8 1.6 - - + -
201B LEU* 3.8 17.9 - - + -
202B VAL 3.4 12.6 - - - +
203B ILE* 4.1 17.7 - - + -
1087C TYR* 3.2 32.1 + + - -
1089C GLU 5.4 3.3 - - - +
1213C TYR* 5.2 12.3 - + - -
1218C GLY 4.2 11.1 + - - -
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Residues in contact with ASN 186 (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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37B HIS* 6.5 0.9 - - - -
185B TYR* 1.3 82.6 - - - +
187B VAL* 1.3 66.8 + - - +
188B GLU* 4.1 16.5 + - - +
201B LEU* 3.4 9.4 - - - +
202B VAL* 3.1 42.8 + - - +
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Residues in contact with VAL 187 (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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36B GLY* 4.2 24.0 - - - +
37B HIS* 4.0 38.1 - - + +
185B TYR* 5.8 1.8 - - + -
186B ASN* 1.3 80.8 - - - +
188B GLU* 1.3 77.8 + - - +
199B ASP* 5.0 12.1 - - + -
200B LYS 3.4 6.1 - - - +
201B LEU* 4.5 6.5 - - + -
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Residues in contact with GLU 188 (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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186B ASN* 4.1 17.1 + - - +
187B VAL* 1.3 85.3 - - - +
189B ALA* 1.3 63.1 + - - +
199B ASP* 3.4 6.6 - - - +
200B LYS* 2.5 64.1 + - - +
202B VAL* 4.2 16.8 - - + -
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Residues in contact with ALA 189 (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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188B GLU* 1.3 78.0 + - - +
190B ALA* 1.3 61.5 + - - +
191B ARG* 4.3 0.7 + - - +
198B LEU 3.7 7.6 - - - +
199B ASP* 5.7 0.4 - - - -
200B LYS* 4.9 5.1 + - - -
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Residues in contact with ALA 190 (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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29B GLU* 5.3 6.3 - - + -
30B PRO* 5.9 4.0 - - + -
188B GLU 3.6 1.4 + - - -
189B ALA* 1.3 74.5 - - - +
191B ARG* 1.3 64.5 + - - +
192B VAL* 4.0 3.6 + - + -
195B ARG 5.5 0.3 - - - +
196B THR* 5.8 0.2 - - - -
197B ASP* 4.9 3.6 + - - -
198B LEU* 3.2 37.5 + - + +
199B ASP 5.0 0.7 - - - -
200B LYS* 4.0 29.8 - - + +
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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