Contacts of the strand formed by residues 175 - 183 (chain B) in PDB entry 4D1Q
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 ALA 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B ALA* 3.8 16.8 - - + +
170B VAL* 3.9 24.2 - - + +
173B ASP 3.8 0.6 - - - -
174B GLY* 1.3 78.4 - - - +
176B SER* 1.3 62.8 + - - +
196B LEU* 4.8 8.1 - - + -
197B HIS 3.4 8.5 - - - +
198B TYR* 4.0 10.5 - - + -
242B SER 3.9 1.6 + - - +
243B ILE* 3.3 20.1 - - + +
244B LYS* 3.4 16.8 + - - +
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Residues in contact with SER 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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175B ALA* 1.3 75.5 - - - +
177B ALA* 1.3 55.8 + - - +
196B LEU* 3.4 4.4 - - - +
197B HIS* 2.6 49.7 + - - +
243B ILE* 3.9 2.9 - - - -
244B LYS* 3.1 29.2 + - - -
563B SER* 3.7 6.9 + - - -
564B ILE* 3.3 39.1 + - - +
565B PRO* 4.0 4.2 - - - +
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER* 1.3 75.1 - - - +
178B THR* 1.3 60.1 + - - +
194B VAL* 4.9 2.0 - - + -
195B THR 2.9 19.1 - - - +
196B LEU* 3.9 13.0 - - + -
197B HIS* 4.0 3.1 - - - -
232B PHE* 4.5 4.9 - - + -
243B ILE* 3.9 2.6 - - + +
244B LYS 2.8 9.7 + - - +
245B PHE* 3.3 31.0 - - + -
246B VAL* 2.9 31.0 + - - +
565B PRO* 5.9 0.4 - - - -
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Residues in contact with THR 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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177B ALA* 1.3 71.8 - - - +
179B ILE* 1.3 68.4 + - - +
194B VAL* 3.4 5.0 - - - +
195B THR* 2.5 44.7 + - - +
197B HIS* 3.1 17.8 + - - -
246B VAL* 3.3 33.5 - - + +
565B PRO* 5.4 0.7 - - + +
567B SER 3.9 3.6 - - - +
568B SER* 3.4 29.4 - - - +
570B ALA* 3.9 4.0 - - + +
571B SER* 3.0 11.9 - - - +
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Residues in contact with ILE 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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178B THR* 1.3 82.8 - - - +
180B ASP* 1.3 71.7 + - - +
192B LEU* 4.3 11.2 - - + -
193B GLY 3.2 6.3 - - - +
194B VAL* 3.6 18.6 - - + -
224B ILE* 5.1 5.4 - - + -
228B LEU* 3.4 35.2 - - + -
245B PHE* 4.2 12.1 - - + -
246B VAL 3.9 3.2 + - - +
247B THR* 3.4 19.5 + - - +
248B ASP* 4.5 1.6 - - - +
253B VAL* 3.4 30.5 - - + -
256B SER* 5.7 0.4 - - - +
257B LEU* 3.9 20.9 - - + -
568B SER* 4.7 3.1 + - - -
571B SER* 3.1 6.5 + - - -
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Residues in contact with ASP 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 ILE* 1.3 80.4 - - - +
181B LEU* 1.3 88.6 + - - +
192B LEU* 3.4 4.4 - - - +
193B GLY 3.2 27.4 + - - -
248B ASP* 3.5 25.8 - - - +
253B VAL* 5.0 6.0 - - - +
268B HIS* 4.7 1.0 + - - -
568B SER* 4.7 4.1 - - - -
571B SER* 4.0 11.1 + - - -
572B GLU* 2.9 26.4 - - - +
575B PHE* 3.2 21.7 - - + -
16F G 5.2 0.7 - - - +
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Residues in contact with LEU 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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180B ASP* 1.3 90.7 + - - +
182B TRP* 1.3 61.5 + - - +
183B THR* 5.6 1.1 - - - -
190B ASN* 4.4 16.4 - - - +
191B PHE 3.2 9.4 - - - +
192B LEU* 3.3 32.8 - - + -
214B LEU* 5.0 4.5 - - + -
219B SER* 3.9 14.8 - - - +
224B ILE* 3.6 36.3 - - + -
252B ASN* 4.6 7.6 - - + +
253B VAL* 4.3 12.7 - - + +
575B PHE* 3.7 5.1 - - - -
16F G 4.9 4.5 + - - -
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Residues in contact with TRP 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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181B LEU* 1.3 72.0 - - - +
183B THR* 1.3 80.5 + - - +
184B ASP* 3.7 34.8 - - + -
185B ASN* 5.2 6.5 - - - -
190B ASN* 3.9 1.1 + - - -
191B PHE* 2.8 64.7 + + + +
211B LEU* 4.6 2.0 - - + -
575B PHE* 3.2 63.2 + + + +
578B ALA* 3.8 26.5 - - + -
579B GLY* 4.3 12.8 - - - -
582B ILE* 4.5 7.9 - - + -
15F T 4.1 3.8 + - - -
16F G 3.8 29.9 + - - -
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Residues in contact with THR 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 LEU 5.6 0.7 - - - -
182B TRP* 1.3 93.6 + - - +
184B ASP* 1.3 69.3 + - - +
185B ASN* 5.2 1.2 - - - +
188B LYS* 4.0 10.4 + - - +
189B ARG 3.1 18.6 + - - -
190B ASN* 3.4 21.5 - - - +
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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