Contacts of the helix formed by residues 269 - 280 (chain C) in PDB entry 5Q0S
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 MET 269 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265C ASN* 5.4 14.8 - - + +
267C GLN 3.4 7.2 + - - +
268C ARG* 1.3 73.5 - - - +
270C PRO* 1.4 87.2 - - + +
271C GLN* 4.3 13.7 - - + +
272C GLU* 2.9 34.0 + - + +
273C ILE* 3.4 7.1 - - - +
335C ARG* 5.8 0.7 - - - +
342C LYS* 5.8 2.9 - - - +
383C GLN* 5.7 6.7 - - - +
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Residues in contact with PRO 270 (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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268C ARG 3.6 0.4 - - - -
269C MET* 1.4 101.1 - - + +
271C GLN* 1.4 60.9 + - - +
273C ILE* 3.1 16.0 + - + +
274C THR* 3.1 19.9 + - - +
335C ARG* 3.6 23.6 - - - +
339C ILE* 3.8 28.7 - - + +
342C LYS* 4.0 40.2 - - + +
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Residues in contact with GLN 271 (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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269C MET* 3.1 11.3 + - + -
270C PRO* 1.4 77.2 - - - +
272C GLU* 1.3 57.3 + - - +
274C THR* 3.6 7.4 - - - +
275C ASN* 3.0 64.3 + - - +
344C LEU* 5.7 7.4 - - + -
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Residues in contact with GLU 272 (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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268C ARG* 3.6 36.9 + - + +
269C MET* 2.9 26.9 + - + +
271C GLN* 1.3 78.1 - - - +
273C ILE* 1.3 58.9 + - - +
275C ASN* 4.4 5.0 - - - +
276C LYS* 3.8 17.7 + - - +
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Residues in contact with ILE 273 (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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268C ARG* 3.9 22.4 - - + +
269C MET 3.4 20.4 - - - +
270C PRO* 3.1 5.3 + - + +
272C GLU* 1.3 75.3 - - - +
274C THR* 1.4 62.4 + - - +
275C ASN 3.3 0.2 - - - -
276C LYS* 3.3 7.0 + - - +
277C ILE* 3.3 33.9 + - + +
294C MET* 3.3 42.6 - - + -
339C ILE* 3.7 26.7 - - + -
501C 9LJ 3.7 36.8 - - + +
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Residues in contact with THR 274 (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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270C PRO* 3.1 14.2 + - + -
271C GLN* 3.6 10.2 - - - +
273C ILE* 1.4 70.4 - - - +
275C ASN* 1.4 62.8 + - - +
277C ILE* 3.4 1.1 + - - +
278C LEU* 2.9 44.5 + - - +
339C ILE* 3.7 29.8 - - + +
344C LEU* 4.4 19.6 - - + +
352C LEU* 3.8 28.5 - - + -
501C 9LJ 3.7 10.3 - - - -
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Residues in contact with ASN 275 (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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271C GLN* 3.0 55.7 + - - +
272C GLU* 4.4 5.2 - - - +
273C ILE 3.3 0.2 - - - -
274C THR* 1.4 77.7 + - - +
276C LYS* 1.4 56.1 + - - +
278C LEU* 3.9 6.1 - - - +
279C LYS* 3.0 36.4 + - + +
344C LEU* 6.2 0.5 - - - +
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Residues in contact with LYS 276 (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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272C GLU 3.8 12.8 + - - +
273C ILE* 3.3 10.1 + - - +
275C ASN* 1.4 80.6 - - - +
277C ILE* 1.3 65.2 + - + +
279C LYS* 3.7 14.4 + - - +
280C GLU 3.9 0.2 - - - +
282C PHE* 3.3 35.3 - - + -
290C ILE* 3.8 42.6 - - + -
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Residues in contact with ILE 277 (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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273C ILE* 3.3 22.7 + - + +
274C THR 3.4 3.8 + - - +
276C LYS* 1.3 76.6 - - + +
278C LEU* 1.4 51.2 + - - +
280C GLU 3.2 10.9 - - - +
282C PHE* 4.7 7.7 - - + -
287C ASN* 5.9 2.9 - - - +
290C ILE* 5.7 6.1 - - + -
352C LEU* 3.9 20.6 - - + +
355C ARG* 2.8 52.7 + - + -
356C ILE* 4.6 6.7 - - + +
501C 9LJ 3.6 61.0 - - + -
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Residues in contact with LEU 278 (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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274C THR* 2.9 26.5 + - - +
275C ASN* 4.2 6.3 - - - +
277C ILE* 1.4 70.5 - - - +
279C LYS* 1.4 61.8 + - - +
344C LEU* 4.2 16.8 - - + -
348C HIS* 3.3 56.5 - - + +
351C LEU* 3.8 26.7 - - + +
352C LEU* 3.6 24.2 - - + +
355C ARG* 2.9 21.7 + - + +
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Residues in contact with LYS 279 (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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275C ASN* 3.0 22.6 + - + +
276C LYS* 3.9 9.2 - - - +
277C ILE 3.4 0.6 - - - -
278C LEU* 1.4 77.5 - - - +
280C GLU* 1.3 86.7 + - + +
355C ARG* 4.3 2.3 + - - -
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Residues in contact with GLU 280 (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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276C LYS* 4.1 0.8 + - - -
277C ILE 3.2 14.6 - - - +
278C LEU 3.5 0.2 - - - -
279C LYS* 1.3 102.2 + - + +
281C ALA* 1.3 64.0 + - - +
282C PHE* 3.3 49.6 - - + -
355C ARG* 3.7 9.9 - - - +
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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