Contacts of the strand formed by residues 184 - 194 (chain B) in PDB entry 3LHD
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 LEU 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B ASN* 4.7 1.0 + - - -
163B VAL* 3.5 14.8 - - + +
164B ASP 3.3 29.8 - - - +
165B HIS* 3.7 11.0 - - - -
166B VAL* 3.9 12.8 - - + +
180B ALA* 2.9 25.1 + - + +
182B LYS 3.5 0.9 - - - +
183B ALA* 1.3 79.0 - - - +
185B LYS* 1.3 69.2 + - - +
186B PRO* 4.4 0.3 - - - +
188B GLY 3.7 15.3 - - - +
189B PHE 3.8 1.8 - - - +
190B PHE* 3.8 25.4 - - + +
214B PHE* 4.1 15.3 - - + -
252B ARG* 3.1 33.5 + - + -
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Residues in contact with LYS 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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60A ARG* 5.9 6.7 - - - +
96B PHE* 6.0 0.2 - - - -
162B ASN* 3.3 44.5 + - + +
163B VAL 2.9 11.3 + - - +
164B ASP* 3.4 36.1 + - - +
183B ALA 3.7 2.2 + - - -
184B LEU* 1.3 79.7 - - - +
186B PRO* 1.3 83.6 - - + +
187B GLY 3.3 0.3 + - - -
188B GLY* 3.1 17.0 + - - +
252B ARG* 3.8 5.0 - - - -
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Residues in contact with PRO 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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44A PHE* 3.7 17.9 - - + +
45A GLY* 3.6 32.5 - - - +
57A LYS* 5.3 1.1 - - - +
59A LEU* 3.6 19.6 - - + +
60A ARG* 5.2 6.9 + - - +
162B ASN* 5.3 5.2 - - - +
184B LEU 4.4 0.2 - - - +
185B LYS* 1.3 95.1 - - + +
187B GLY* 1.3 59.6 + - - +
188B GLY 3.2 0.4 + - - -
252B ARG* 3.7 26.4 - - - +
253B ILE 4.4 3.1 - - - +
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Residues in contact with GLY 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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59A LEU* 3.5 13.5 - - - +
60A ARG 5.8 1.6 - - - -
62A ARG* 4.7 9.6 + - - +
165B HIS* 5.5 0.7 - - - -
186B PRO* 1.3 71.7 - - - +
188B GLY* 1.3 60.3 + - - +
189B PHE* 3.9 7.1 - - - -
251B ARG* 3.3 45.5 + - - +
252B ARG 3.1 14.3 + - - -
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Residues in contact with GLY 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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163B VAL 4.8 1.1 - - - -
164B ASP* 3.1 18.2 - - - -
165B HIS* 4.9 0.9 - - - -
184B LEU* 3.7 8.2 - - - +
185B LYS* 3.1 17.0 + - - +
186B PRO 3.2 1.4 + - - -
187B GLY* 1.3 79.5 - - - +
189B PHE* 1.3 62.7 + - - -
190B PHE 3.8 0.5 + - - -
251B ARG* 3.8 0.2 - - - -
252B ARG* 2.9 30.0 + - - +
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Residues in contact with PHE 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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62A ARG* 6.1 2.0 - - + -
64A VAL* 4.2 15.9 - - + -
88B TYR 4.0 15.3 - - - -
89B ALA* 3.3 42.0 - - + -
164B ASP 3.1 7.9 + - - -
165B HIS* 3.3 18.5 + + - +
166B VAL 3.0 25.8 + - - +
184B LEU* 4.0 3.4 - - - -
187B GLY 3.9 6.7 - - - -
188B GLY* 1.3 71.6 - - - -
190B PHE* 1.3 60.1 + - - +
191B VAL* 4.0 5.4 - - + +
249B PHE* 4.4 15.5 - + + -
250B ALA 3.6 16.4 - - - -
251B ARG* 3.2 46.7 - - + -
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Residues in contact with PHE 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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166B VAL* 3.8 7.2 - - + -
168B LEU* 3.6 27.1 - - + -
173B PRO 3.8 20.0 - - - -
176B VAL 4.5 0.4 - - - -
177B VAL* 4.0 15.7 - - + -
180B ALA* 3.6 29.2 - - + -
184B LEU* 3.8 7.9 - - + +
189B PHE* 1.3 73.0 - - - +
191B VAL* 1.3 65.8 + - - +
192B ALA* 4.2 15.0 - - + -
203B LEU* 3.7 26.7 - - + -
207B LEU* 4.2 10.1 - - + -
214B PHE* 3.8 21.3 - + + -
248B THR* 5.2 2.0 - - + -
249B PHE* 3.5 1.0 - - - -
250B ALA* 2.7 56.9 + - + +
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Residues in contact with VAL 191 (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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85B ILE* 3.8 25.4 - - + -
89B ALA* 4.0 15.0 - - + -
165B HIS* 5.7 0.2 - - + -
166B VAL 2.9 13.8 + - - +
167B ILE* 4.2 15.0 - - + -
168B LEU* 2.8 33.7 + - - +
189B PHE* 4.0 9.6 - - + +
190B PHE* 1.3 83.1 - - - +
192B ALA* 1.3 58.9 + - - +
247B ILE* 3.8 25.6 - - + -
248B THR 3.4 4.9 - - - +
249B PHE* 3.6 24.5 - - + -
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Residues in contact with ALA 192 (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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168B LEU* 3.5 6.3 - - + +
173B PRO* 3.8 24.2 - - + -
190B PHE* 4.2 8.5 - - + -
191B VAL* 1.3 75.6 - - - +
193B TYR* 1.3 60.4 + - - +
194B THR* 4.2 2.5 + - + +
203B LEU* 3.7 30.3 - - + -
246B TYR 3.7 0.5 - - - +
247B ILE* 3.2 8.9 - - - +
248B THR* 2.9 32.8 + - - +
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Residues in contact with TYR 193 (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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76B ILE 4.4 9.4 + - - -
77B VAL* 3.6 32.1 - - + -
78B HIS* 4.8 0.3 - - - -
81B ASP* 3.4 28.6 + - + -
85B ILE* 5.1 9.6 - - + -
107B LEU* 6.2 0.9 - - + -
168B LEU 2.8 15.8 + - - +
169B ASP* 3.8 25.4 - - + -
170B LEU 4.4 4.3 - - - +
173B PRO* 5.5 0.3 - - - +
192B ALA* 1.3 72.5 - - - +
194B THR* 1.3 63.7 + - - +
195B PRO* 4.0 21.8 - - + +
244B THR* 3.2 28.2 + - - -
245B GLY* 3.7 17.7 - - - -
246B TYR 3.3 11.4 - - - -
247B ILE* 4.1 14.4 - - + +
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Residues in contact with THR 194 (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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170B LEU 5.1 0.2 - - - +
173B PRO* 3.8 29.6 - - + -
192B ALA* 4.6 5.8 + - + +
193B TYR* 1.3 81.5 - - - +
195B PRO* 1.3 65.8 - - - +
196B CYS 3.4 0.5 + - - -
199B GLN* 3.6 33.9 - - + +
200B VAL* 3.2 22.5 - - - +
203B LEU* 4.6 6.1 - - + -
245B GLY* 4.0 0.7 - - - -
246B TYR* 2.7 41.7 + - - +
248B THR* 5.0 2.6 + - - -
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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