Contacts of the strand formed by residues 316 - 322 (chain E) in PDB entry 3KQG
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 316 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E SER* 3.3 22.0 - - - +
211E LEU* 3.6 34.1 - - + +
212E ILE 3.7 10.1 - - - -
213E PRO* 3.8 9.9 - - + +
249E LEU* 3.8 25.1 - - + -
250E ILE 3.6 8.0 + - - +
251E TYR* 3.0 37.2 - - + +
252E TRP* 2.7 28.4 + - - -
315E PHE* 1.3 77.1 - - - +
317E PHE* 1.3 53.1 + - - +
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Residues in contact with PHE 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E TYR* 3.2 4.1 - + - +
210E SER* 2.9 47.9 + - - -
212E ILE* 3.4 23.6 - - + -
214E LYS* 3.9 20.0 - - + -
219E ALA* 3.4 28.7 - - + -
222E PHE* 3.3 50.9 - + + -
223E CYS* 3.8 19.1 - - - -
230E LEU* 3.7 9.4 - - + -
251E TYR* 3.7 3.0 - - - -
252E TRP* 3.6 11.4 - - + +
315E PHE 4.1 4.9 - - - +
316E LEU* 1.3 77.1 - - - +
318E ILE* 1.3 62.9 + - - +
319E CYS* 3.7 9.6 - - - -
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Residues in contact with ILE 318 (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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207E TYR* 4.2 4.9 - - + -
208E TYR 3.2 6.1 - - - +
209E PHE* 3.5 33.7 - - + -
230E LEU* 3.3 9.5 - - - +
231E THR* 2.8 47.1 + - + +
242E LEU* 4.1 23.3 - - + +
246E ALA* 5.1 0.2 - - + -
251E TYR* 3.4 35.0 - - + -
252E TRP 3.1 9.1 + - - +
253E ILE* 4.3 11.7 - - + -
298E ILE* 4.8 9.2 - - + -
317E PHE* 1.3 74.4 - - - +
319E CYS* 1.3 66.9 + - - +
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Residues in contact with CYS 319 (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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199E TRP* 4.4 4.9 - - + -
207E TYR* 3.2 8.9 - - - +
208E TYR* 2.9 44.8 + - + -
222E PHE* 4.1 8.1 - - - -
223E CYS* 2.1 51.6 - - - -
228E SER* 3.4 13.2 - - - +
229E HIS 3.3 5.4 - - - -
317E PHE* 3.7 17.5 - - - -
318E ILE* 1.3 75.4 - - - +
320E LYS* 1.3 63.0 + - - +
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Residues in contact with LYS 320 (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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205E ASN* 3.5 32.8 - - + +
206E PHE 3.3 7.2 - - - +
207E TYR* 3.6 11.9 - - + -
228E SER* 3.1 13.4 - - - -
229E HIS* 2.8 18.7 + - - +
231E THR* 3.2 33.2 - - - +
232E SER* 3.4 24.3 + - - +
234E THR* 4.5 7.1 + - - +
238E GLU* 2.9 28.5 + - - +
268E ASP* 4.8 6.0 - - - +
270E THR* 5.5 0.4 + - - -
319E CYS* 1.3 77.8 - - - +
321E ARG* 1.3 64.6 + - - +
322E PRO* 4.7 1.9 - - + +
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Residues in contact with ARG 321 (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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194E VAL* 3.9 28.3 - - - +
199E TRP* 3.5 32.6 - - + -
205E ASN* 4.2 3.8 - - - -
206E PHE* 2.8 64.8 + - + +
226E ARG 3.8 18.6 + - - -
227E ASN* 3.5 15.4 + - - +
228E SER* 3.5 12.3 - - - -
320E LYS* 1.3 73.6 - - - +
322E PRO* 1.3 77.5 + - + +
323E TYR* 5.6 0.2 - - - +
324E VAL* 5.9 2.0 - - - +
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Residues in contact with PRO 322 (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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204E GLY 4.5 1.3 - - - +
205E ASN* 3.3 18.3 - - - +
206E PHE* 4.3 3.8 - - - -
227E ASN 5.5 0.9 - - - +
320E LYS* 4.7 2.0 - - + +
321E ARG* 1.3 98.6 + - + +
323E TYR* 1.3 64.0 + - - +
324E VAL* 3.5 11.5 + - + +
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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