Contacts of the strand formed by residues 176 - 183 (chain G) 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 SER 176 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175G ALA* 1.3 74.1 - - - +
177G ALA* 1.3 59.1 + - - +
196G LEU* 3.3 2.6 - - - +
197G HIS* 2.5 45.2 + - - +
244G LYS* 3.2 9.9 + - - -
560G SER 4.2 1.0 + - - -
563G SER* 3.2 10.5 + - - -
564G ILE* 3.0 36.8 + - - +
565G PRO* 3.3 28.0 - - - -
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Residues in contact with ALA 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G SER* 1.3 75.3 - - - +
178G THR* 1.3 62.4 + - - +
194G VAL* 4.9 2.5 - - + -
195G THR 3.2 13.9 - - - +
196G LEU* 3.9 11.4 - - + -
197G HIS* 4.5 1.3 - - - -
232G PHE* 4.5 7.2 - - + -
243G ILE* 3.9 5.6 - - + +
244G LYS 2.9 7.1 + - - -
245G PHE* 3.2 35.8 - - + +
246G VAL* 2.8 28.6 + - - +
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Residues in contact with THR 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G ALA* 1.3 76.1 - - - +
179G ILE* 1.3 67.0 + - - +
194G VAL* 3.5 6.6 - - - +
195G THR* 2.7 45.8 + - - +
197G HIS* 4.3 4.6 + - - -
246G VAL* 3.3 15.1 + - - +
565G PRO* 4.3 2.1 - - - +
567G SER 3.7 14.7 + - - -
568G SER* 3.2 38.1 - - - +
570G ALA* 3.8 6.9 - - - +
571G SER* 3.1 20.3 + - - +
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Residues in contact with ILE 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177G ALA 4.3 0.4 + - - -
178G THR* 1.3 80.7 - - - +
180G ASP* 1.3 65.6 + - - +
192G LEU* 4.2 16.4 - - + -
193G GLY 3.4 15.7 - - - +
194G VAL* 3.8 10.8 - - + -
224G ILE* 5.2 4.3 - - + -
228G LEU* 3.3 45.3 - - + -
245G PHE* 4.6 12.3 - - + -
246G VAL 3.5 4.8 + - - -
247G THR* 3.6 17.8 + - - +
248G ASP* 3.6 11.8 - - - +
253G VAL* 3.4 32.7 - - + +
257G LEU* 4.6 4.7 - - + -
568G SER* 4.5 1.2 - - - -
571G SER* 3.8 2.5 - - - -
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Residues in contact with ASP 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G ILE* 1.3 76.5 - - - +
181G LEU* 1.3 87.8 + - - +
192G LEU* 3.6 6.1 - - - +
193G GLY 2.9 30.9 + - - -
248G ASP* 2.9 28.6 - - - +
253G VAL* 5.3 3.3 - - - +
268G HIS* 4.4 0.9 + - - -
568G SER* 4.4 3.3 + - - -
571G SER* 3.8 11.5 + - - -
572G GLU* 3.0 28.8 - - - +
575G PHE* 3.4 20.7 - - + -
16J G 5.1 2.1 - - - +
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Residues in contact with LEU 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G ASP* 1.3 91.4 + - - +
182G TRP* 1.3 62.9 + - - +
190G ASN* 4.8 9.4 - - - +
191G PHE 3.1 21.1 - - - +
192G LEU* 3.7 24.9 - - + -
214G LEU* 3.9 25.6 - - + -
219G SER* 4.8 6.5 - - - +
224G ILE* 3.5 35.7 - - + -
252G ASN* 5.1 4.0 - - + -
253G VAL* 3.7 19.1 - - + -
575G PHE* 4.0 2.4 - - - -
16J G 4.9 3.1 + - - -
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Residues in contact with TRP 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G LEU* 1.3 75.6 - - - +
183G THR* 1.3 69.7 + - - +
184G ASP* 3.8 27.4 - - + -
185G ASN* 5.4 2.5 - - - -
190G ASN* 3.9 2.4 + - - -
191G PHE* 2.7 80.4 + + + +
211G LEU* 4.7 0.9 - - + -
575G PHE* 3.6 55.8 - + + +
578G ALA* 4.1 23.1 - - + -
579G GLY* 4.4 12.8 - - - -
582G ILE* 4.8 5.8 - - + -
15J T 3.9 10.3 + - - -
16J G 2.9 35.2 + - - +
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Residues in contact with THR 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G TRP* 1.3 91.2 + - - +
184G ASP* 1.3 65.8 + - - +
185G ASN* 3.8 1.7 + - - +
188G LYS* 3.8 16.5 + - + +
189G ARG 2.7 24.4 + - - -
190G ASN* 3.5 15.8 + - - +
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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