Contacts of the strand formed by residues 174 - 186 (chain B) in PDB entry 5X22
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 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.4 33.2 - - + +
45B LEU* 4.2 7.3 - - + +
48B ILE* 4.4 8.3 - - + -
172B SER* 2.8 24.0 + - - +
173B PRO* 1.3 79.3 - - + +
175B ARG* 1.3 64.8 + - - +
176B ARG 3.9 7.2 - - - +
177B VAL* 3.5 29.8 - - + -
199B ILE* 4.4 4.5 - - + -
200B TRP 3.7 9.9 - - - +
201B THR* 4.2 5.8 - - + +
210B ALA* 4.0 26.7 - - + -
851D LEU* 4.6 6.9 - - - +
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Residues in contact with ARG 175 (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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19B GLU* 5.9 0.2 - - - -
45B LEU* 5.1 3.9 - - - +
83B LYS 5.3 2.0 + - - -
84B GLU* 4.4 17.1 + - - +
86B VAL* 3.9 25.5 - - - +
170B VAL* 5.5 9.3 - - - +
172B SER 5.4 2.5 - - - +
173B PRO 3.5 1.1 + - - +
174B VAL* 1.3 76.3 - - - +
176B ARG* 1.3 60.7 + - - +
200B TRP* 2.5 20.7 + - + +
201B THR 4.0 17.7 - - - -
202B ASP* 3.6 20.4 + - + +
845D ASN* 4.4 22.4 + - - +
847D ASP* 4.0 42.5 - - + +
848D GLU* 5.8 1.6 - - - +
851D LEU* 5.0 8.0 - - - +
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Residues in contact with ARG 176 (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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45B LEU* 4.8 3.1 - - - -
174B VAL* 3.6 2.3 - - - +
175B ARG* 1.3 81.7 - - + +
177B VAL* 1.3 77.4 + - - +
178B ALA* 4.4 10.1 - - - +
198B ARG* 5.8 0.8 - - - +
199B ILE* 3.6 0.5 - - - -
200B TRP* 2.9 86.2 + - + +
847D ASP* 4.5 8.1 + - - +
884D ARG* 3.2 47.0 - - - +
888D GLU* 2.3 38.9 + - - -
937D TYR* 5.1 7.3 + - - -
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Residues in contact with VAL 177 (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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41B ARG* 3.6 53.0 + - + -
44B LEU* 3.7 27.8 - - + -
45B LEU* 4.1 14.2 - - + +
174B VAL* 3.5 21.1 - - + -
176B ARG* 1.3 85.2 - - - +
178B ALA* 1.3 71.1 + - - +
179B PHE* 5.4 0.2 - - + -
197B LEU* 4.2 14.8 - - + -
198B ARG 3.5 4.0 - - - +
199B ILE* 4.6 4.9 - - + -
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Residues in contact with ALA 178 (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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41B ARG* 5.4 0.9 - - - +
176B ARG* 4.4 12.6 - - - +
177B VAL* 1.3 76.4 - - - +
179B PHE* 1.3 63.2 + - - +
197B LEU* 3.6 3.3 - - - +
198B ARG* 2.9 44.7 + - + +
200B TRP* 4.0 20.5 - - + -
937D TYR* 6.0 2.2 - - - +
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Residues in contact with PHE 179 (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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34B VAL* 4.1 9.4 - - + -
37B GLY* 3.9 19.1 - - - -
38B ASN* 3.2 40.8 - - - -
41B ARG* 4.3 22.0 - - + -
178B ALA* 1.3 77.7 - - - +
180B GLN* 1.3 61.4 + - - +
181B VAL* 3.8 21.5 - - + -
195B LEU* 3.7 19.3 - - + -
196B THR 3.2 12.6 - - - +
197B LEU* 3.5 16.2 - - + -
198B ARG* 4.8 1.6 - - - +
936D TYR* 4.5 8.1 + - - -
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Residues in contact with GLN 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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179B PHE* 1.3 77.0 - - - +
181B VAL* 1.3 67.3 + - - +
182B GLU* 3.8 34.1 + - + +
194B LYS 3.6 2.3 - - - +
196B THR* 2.9 42.1 + - + +
638D LYS* 5.1 10.5 - - - +
936D TYR* 4.2 35.9 + - + +
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Residues in contact with VAL 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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33B GLY* 3.5 31.6 - - - +
34B VAL* 3.6 12.3 - - + +
179B PHE* 3.8 17.0 - - + -
180B GLN* 1.3 78.1 + - - +
182B GLU* 1.3 65.6 + - - +
183B ASP 4.1 0.5 + - - -
193B ASP* 3.6 38.8 - - + +
194B LYS 3.4 6.7 - - - +
195B LEU* 4.0 4.7 - - + -
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Residues in contact with GLU 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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180B GLN* 3.8 35.2 + - + +
181B VAL* 1.3 76.3 - - - +
183B ASP* 1.3 67.1 + - - +
193B ASP* 3.8 0.9 - - - -
194B LYS* 2.9 64.7 + - + +
196B THR* 4.5 10.3 + - - -
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Residues in contact with ASP 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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181B VAL 4.1 1.6 + - - -
182B GLU* 1.3 74.6 - - - +
184B THR* 1.3 60.4 + - - +
190B THR 4.6 2.6 - - - +
191B ASP* 3.1 15.8 - - - +
192B LEU 3.0 6.5 + - - +
193B ASP* 5.3 0.2 - - - -
2001B MG 2.2 33.4 - - - -
851C LYS* 5.8 3.9 + - - -
636D GLN* 6.0 6.5 - - + -
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Residues in contact with THR 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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26B GLU* 4.1 13.5 + - - +
27B PRO* 4.7 9.9 - - + -
182B GLU* 6.1 0.2 - - - -
183B ASP* 1.3 76.7 - - - +
185B ARG* 1.3 70.6 + - - +
190B THR 2.8 20.7 - - - +
192B LEU* 2.9 40.2 + - + +
193B ASP 3.8 9.0 - - - +
194B LYS* 3.7 31.1 - - + +
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Residues in contact with ARG 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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27B PRO* 6.1 0.4 - - - -
184B THR* 1.3 88.0 + - - +
186B LEU* 1.3 63.0 + - - +
187B GLY* 3.2 30.4 + - - +
189B ARG 3.2 15.0 - - - +
190B THR* 3.6 13.9 - - - +
192B LEU* 4.6 2.7 - - - -
689D ASP* 3.2 27.3 + - - -
692D GLU* 3.6 34.6 + - - +
51E LEU* 5.2 5.7 - - - +
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Residues in contact with LEU 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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6B LEU* 5.4 5.4 - - + -
7B LYS 5.0 9.4 - - - +
27B PRO* 3.9 29.4 - - + -
185B ARG* 1.3 75.4 - - - +
187B GLY* 1.3 63.8 + - - +
188B GLN 3.2 0.5 + - - -
189B ARG* 2.9 36.5 + - + +
192B LEU* 3.8 18.3 - - + +
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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