Contacts of the helix formed by residues 183 - 192 (chain E) in PDB entry 6GYS
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 PRO 183 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181E LEU 3.5 9.2 - - - +
182E CYS* 1.3 85.1 - - - +
184E PRO* 1.3 72.3 - - + +
185E LEU* 4.5 3.1 - - + +
186E LEU* 3.7 32.1 - - + +
187E LYS* 3.2 26.4 + - + +
517E LEU* 3.9 16.8 - - + -
520E PHE* 3.6 32.1 - - + -
524E TYR* 3.9 11.2 - - + +
533E LEU* 5.5 1.6 - - + -
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Residues in contact with PRO 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E CYS 3.4 8.7 - - - +
183E PRO* 1.3 85.6 - - + +
185E LEU* 1.3 62.0 + - - +
188E VAL* 3.3 23.4 + - - +
218E PHE* 3.3 8.1 - - + -
346E PHE* 4.5 3.1 - - + -
351E LEU* 3.9 25.5 - - + +
358E TYR* 4.9 13.0 - - - +
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Residues in contact with LEU 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E PRO* 3.1 5.1 - - + -
184E PRO* 1.3 83.0 - - - +
186E LEU* 1.3 54.0 + - + +
188E VAL* 3.2 2.3 + - - +
189E SER* 2.5 51.0 + - - +
218E PHE* 3.5 13.1 - - + -
219E GLN* 4.6 8.7 - - + -
222E SER* 3.4 31.2 - - - +
223E TYR* 5.2 7.2 - - + +
280E ILE* 3.8 35.7 - - + -
409E PHE* 4.1 28.5 - - + -
517E LEU* 5.3 6.5 - - + -
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Residues in contact with LEU 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E PRO* 3.2 26.7 + - + +
185E LEU* 1.3 77.7 - - + +
187E LYS* 1.3 61.3 + - - +
189E SER* 3.8 3.8 - - - -
190E LEU* 2.9 46.5 + - + +
277E CYS* 4.6 14.8 - - - -
279E PHE* 5.1 2.5 - - + -
280E ILE* 3.7 25.4 - - + -
516E ILE* 4.6 23.1 - - + +
517E LEU* 5.3 7.0 - - + -
524E TYR* 4.9 7.6 - - + -
530E PHE* 5.4 6.1 - - + -
533E LEU* 4.2 24.6 - - + +
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Residues in contact with LYS 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E GLN* 4.6 6.1 - - - +
182E CYS* 3.5 30.5 - - - +
183E PRO* 3.2 16.9 + - + +
186E LEU* 1.3 77.2 - - - +
188E VAL* 1.3 61.8 + - - +
191E ASN* 2.6 48.6 + - - +
349E CYS* 3.3 30.4 + - + +
351E LEU* 4.9 3.4 - - + -
524E TYR* 5.3 2.0 - - - -
532E SER* 4.4 4.5 + - - -
533E LEU* 3.7 40.8 - - + +
535E ILE* 5.9 1.8 - - + -
199L HIS* 3.6 29.6 + - + -
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Residues in contact with VAL 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E PRO 3.3 15.6 + - - +
185E LEU 3.2 7.9 + - - +
186E LEU 3.2 0.2 - - - -
187E LYS* 1.3 77.5 - - - +
189E SER* 1.3 60.6 + - - +
191E ASN* 3.2 2.9 + - - +
192E LEU* 2.9 42.0 + - + +
214E PHE* 4.4 5.6 - - + -
215E LEU* 5.2 0.7 - - + -
218E PHE* 3.7 23.8 - - + -
345E VAL* 3.8 21.3 - - + -
346E PHE* 3.5 29.4 - - + -
349E CYS* 3.7 18.2 - - - -
351E LEU* 4.2 4.5 - - + -
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Residues in contact with SER 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU* 2.5 48.0 + - - +
186E LEU 3.0 2.9 + - - -
188E VAL* 1.3 71.7 - - - +
190E LEU* 1.3 63.6 + - - +
192E LEU* 3.0 15.1 + - - +
193E TRP* 3.0 17.8 + - - -
215E LEU* 3.9 17.9 - - - +
218E PHE* 3.9 5.5 - - - -
219E GLN* 4.7 1.5 + - - -
279E PHE 3.7 8.5 - - - -
280E ILE* 3.7 22.6 - - - +
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Residues in contact with LEU 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E LEU* 2.9 26.6 + - + +
189E SER* 1.3 72.7 - - - +
191E ASN* 1.3 58.2 + - - +
193E TRP* 3.0 27.7 + - - +
279E PHE* 3.9 33.2 + - + -
478E PHE* 5.0 2.5 - - + -
479E PHE* 3.8 14.6 - - + -
530E PHE* 3.6 47.6 - - + +
533E LEU* 3.8 28.9 - - + -
534E LEU* 4.0 17.5 - - + -
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Residues in contact with ASN 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E LYS* 2.6 36.7 + - - +
188E VAL 3.2 4.2 + - - +
190E LEU* 1.3 76.1 - - - +
192E LEU* 1.3 64.7 + - + +
193E TRP 3.4 0.2 - - - -
194E ASN* 4.0 15.8 - - - +
197E THR* 5.2 7.1 - - - +
348E TYR* 4.6 18.4 - - + -
349E CYS* 4.1 11.3 - - - -
533E LEU* 2.6 32.7 + - - +
534E LEU* 3.3 25.0 - - - +
535E ILE* 4.0 7.9 + - - +
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Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E VAL* 2.9 36.0 + - + +
189E SER 3.0 11.1 + - - +
191E ASN* 1.3 79.8 - - + +
193E TRP* 1.3 62.8 + - - +
194E ASN 3.2 8.5 + - - +
197E THR* 5.6 3.1 - - + -
205E PHE* 5.6 3.1 - - + -
211E LYS* 3.9 50.9 - - + +
212E LEU* 5.2 5.5 - - - +
214E PHE* 4.0 18.8 - - + -
215E LEU* 4.1 21.3 - - + -
345E VAL* 4.0 20.6 - - + -
348E TYR* 6.5 0.9 - - + -
349E CYS* 6.0 0.9 - - - -
482E HIS* 5.5 1.6 + - - -
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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