Contacts of the helix formed by residues 317 - 329 (chain C) in PDB entry 4K9P
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 ASP 317 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C ALA* 4.8 10.2 - - - +
181C SER* 3.5 21.5 + - - +
182C SER* 3.9 16.9 + - - -
183C VAL* 2.9 26.3 + - - +
300C CYS* 4.8 4.6 - - - +
316C ALA* 1.3 70.6 - - - +
318C ILE* 1.3 67.4 + - - +
319C GLY* 3.2 7.9 + - - -
320C ALA* 2.9 26.7 + - + +
321C MET* 3.0 26.0 + - - +
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Residues in contact with ILE 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ASP* 3.8 39.0 - - + +
211C VAL* 3.9 25.6 - - + -
214C ALA* 4.2 6.0 - - + +
216C ALA* 4.5 4.9 - - + -
273C ILE* 4.0 8.7 - - + +
274C GLY* 3.8 10.1 - - - +
298C VAL* 3.7 40.4 - - + +
300C CYS* 4.1 22.7 - - + +
316C ALA 3.5 1.1 + - - +
317C ASP* 1.3 73.2 + - - +
319C GLY* 1.3 58.5 + - - +
321C MET* 4.1 2.0 - - - +
322C ALA* 2.9 30.6 + - + +
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Residues in contact with GLY 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C ALA* 3.7 23.0 - - - +
216C ALA* 4.3 8.3 - - - -
219C ASP* 4.4 3.3 - - - +
317C ASP* 3.2 8.0 + - - -
318C ILE* 1.3 77.8 - - - +
320C ALA* 1.3 60.4 - - - +
322C ALA* 4.0 1.4 - - - +
323C SER* 3.2 24.8 + - - -
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C SER* 4.3 13.9 + - - +
183C VAL 3.6 24.9 - - - +
184C ARG* 3.9 15.4 - - + +
317C ASP* 2.9 15.3 + - + +
319C GLY* 1.3 75.1 - - - +
321C MET* 1.3 62.2 + - - +
323C SER* 3.5 4.9 + - - -
324C ALA* 3.1 23.9 + - - +
186D ASN* 4.5 9.4 - - + -
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Residues in contact with MET 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ARG* 3.8 7.4 - - + -
185C LEU* 3.5 34.1 - - + -
190C LEU* 4.2 14.6 - - + -
193C LEU* 4.2 11.0 - - + -
273C ILE* 6.4 0.9 - - + -
298C VAL* 3.9 26.5 - - + -
314C ILE* 4.7 5.2 - - + -
316C ALA* 3.6 21.8 - - + -
317C ASP 3.0 20.2 + - - +
318C ILE 4.1 2.0 - - - +
320C ALA* 1.3 75.2 - - - +
322C ALA* 1.3 66.0 + - - +
324C ALA* 3.4 3.2 + - - +
325C LEU* 3.0 63.1 + - + +
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ALA* 3.8 23.1 - - + -
219C ASP* 3.9 11.2 - - + +
220C CYS* 4.5 14.6 - - - +
223C LEU* 5.3 3.2 - - + +
273C ILE* 5.2 9.5 - - + +
318C ILE* 2.9 21.7 + - + +
319C GLY 4.0 0.7 - - - +
321C MET* 1.3 76.4 - - - +
323C SER* 1.3 58.6 + - - +
325C LEU* 4.0 6.5 - - - +
326C ALA* 3.0 32.7 + - - +
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Residues in contact with SER 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ASP* 3.5 24.9 + - - -
319C GLY 3.2 17.1 + - - -
320C ALA* 3.8 5.6 - - - -
321C MET 3.2 0.2 - - - -
322C ALA* 1.3 78.1 - - - +
324C ALA* 1.3 65.6 + - - +
326C ALA* 3.5 0.3 + - - +
327C ASN* 2.7 37.7 + - - -
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Residues in contact with ALA 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ARG* 4.9 13.0 - - + +
190C LEU* 4.2 25.8 - - + -
320C ALA 3.1 15.9 + - - +
321C MET* 3.8 5.8 - - - +
323C SER* 1.3 79.2 - - - +
325C LEU* 1.3 63.1 + - - +
327C ASN* 3.2 5.2 + - - +
328C LEU* 3.0 31.0 + - + +
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Residues in contact with LEU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C LEU* 4.0 13.7 - - + -
193C LEU* 3.8 28.3 - - + -
194C VAL* 4.3 9.2 - - + -
197C LEU* 4.1 15.5 - - + -
223C LEU* 4.1 17.9 - - + -
271C LEU* 4.5 21.5 - - + -
273C ILE* 4.9 5.6 - - + -
298C VAL* 4.8 7.4 - - + -
321C MET* 3.0 41.7 + - + +
322C ALA* 4.1 3.4 - - - +
324C ALA* 1.3 75.3 - - - +
326C ALA* 1.3 64.1 + - - +
327C ASN 3.0 1.2 + - - -
328C LEU* 3.1 12.3 + - - +
329C VAL* 3.1 20.8 + - + +
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Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ASP* 3.2 31.2 - - + +
222C MET* 3.4 24.3 - - + +
223C LEU* 4.0 19.0 - - + +
226C ARG* 3.0 18.9 + - - +
322C ALA 3.0 21.0 + - - +
323C SER 3.9 4.0 - - - +
324C ALA 3.3 0.2 - - - -
325C LEU* 1.3 76.2 - - - +
327C ASN* 1.3 60.4 + - - +
329C VAL* 4.3 1.4 - - - +
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Residues in contact with ASN 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ASP* 4.7 4.8 + - - -
222C MET* 3.4 22.8 - - - +
226C ARG* 3.4 19.5 + - - +
323C SER* 2.7 36.0 + - - +
324C ALA* 3.2 4.9 + - - +
325C LEU 3.0 0.4 - - - -
326C ALA* 1.3 80.3 - - - +
328C LEU* 1.3 62.5 + - + +
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Residues in contact with LEU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C LEU* 3.5 38.1 - - + -
191C ASP* 5.0 8.1 - - - +
194C VAL* 3.9 28.6 - - + +
226C ARG* 4.1 0.2 - - - -
324C ALA* 3.0 20.8 + - + +
325C LEU* 3.1 2.0 + - - +
327C ASN* 1.3 82.8 - - - +
329C VAL* 1.3 68.3 + - - +
330C GLU* 3.5 5.4 + - - +
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Residues in contact with VAL 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C VAL* 4.2 14.1 - - + -
197C LEU* 4.2 27.1 - - + -
198C ASN* 3.7 13.2 - - - +
223C LEU* 3.7 24.9 - - + -
226C ARG* 2.6 56.9 + - + +
227C LEU* 4.2 7.6 - - + -
325C LEU* 3.1 20.6 + - - +
326C ALA 4.3 2.5 - - - +
328C LEU* 1.3 76.8 - - - +
330C GLU* 1.3 61.4 + - - +
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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