Contacts of the helix formed by residues 280 - 288 (chain C) in PDB entry 1U7F
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 ASN 280 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240C LEU* 5.8 4.5 - - + -
278C ASN 3.7 4.1 + - - +
279C ARG* 1.3 78.5 - - - +
281C ALA* 1.3 82.7 + - - +
282C ALA* 2.9 19.4 + - + +
283C VAL* 3.5 19.0 + - + +
284C GLU* 3.0 29.1 + - - +
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Residues in contact with ALA 281 (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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280C ASN* 1.3 83.8 + - - +
282C ALA* 1.3 53.8 + - - +
284C GLU* 3.1 8.5 + - - +
285C LEU* 2.6 38.0 + - - +
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Residues in contact with ALA 282 (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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280C ASN* 2.9 12.4 + - - +
281C ALA* 1.3 75.5 - - - +
283C VAL* 1.3 58.4 + - + +
285C LEU* 2.8 13.9 + - - +
286C THR* 2.7 39.7 + - - +
386C ARG* 6.3 0.9 - - - +
393C PRO* 4.6 9.9 - - + -
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Residues in contact with VAL 283 (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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239C GLU* 3.1 47.6 - - + +
240C LEU* 4.4 20.6 - - + -
279C ARG* 3.9 8.7 - - + +
280C ASN* 3.6 25.8 - - + +
281C ALA 3.3 0.2 - - - -
282C ALA* 1.3 77.4 - - + +
284C GLU* 1.3 64.5 + - - +
286C THR* 3.2 1.4 + - - -
287C ARG* 2.9 30.6 + - + +
393C PRO* 3.7 27.1 - - + +
394C CYS* 4.1 0.6 - - - -
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Residues in contact with GLU 284 (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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492B VAL* 5.6 0.5 - - - +
493B ASP* 3.0 46.2 - - + +
494B ASP* 4.3 11.6 - - - +
497B ARG* 3.8 17.4 + - - -
279C ARG* 3.7 23.2 - - - +
280C ASN 3.0 16.1 + - - +
281C ALA* 3.4 7.6 - - - +
283C VAL* 1.3 77.3 - - - +
285C LEU* 1.3 63.4 + - - +
287C ARG* 3.4 12.2 + - - +
288C ARG* 3.5 10.6 + - - +
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Residues in contact with LEU 285 (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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281C ALA 2.6 17.4 + - - +
282C ALA* 2.8 15.2 + - - +
284C GLU* 1.3 74.7 - - - +
286C THR* 1.3 61.5 + - - +
288C ARG* 3.1 45.7 - - - +
289C HIS* 3.0 28.2 + - + -
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Residues in contact with THR 286 (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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282C ALA* 2.7 21.5 + - - +
283C VAL 3.8 3.1 - - - -
285C LEU* 1.3 71.2 - - - +
287C ARG* 1.3 67.0 + - - +
288C ARG 3.0 2.0 - - - -
289C HIS* 2.9 19.0 + - - +
290C ILE* 3.6 8.5 + - + +
376C PHE 3.6 9.0 - - - +
377C VAL* 3.3 36.8 - - + +
378C LYS* 4.8 7.4 - - + +
393C PRO* 3.7 23.4 - - + +
394C CYS* 4.0 16.2 - - - -
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Residues in contact with ARG 287 (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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492B VAL* 4.6 10.8 - - + +
493B ASP* 2.3 47.5 + - - +
237C TYR* 3.4 8.9 + - - +
239C GLU* 2.9 17.0 + - - -
259C GLY* 4.9 4.9 - - - +
271C LEU* 2.8 23.2 + - - -
272C GLY* 3.6 16.5 + - - -
274C LEU* 2.5 29.1 + - - +
279C ARG* 2.6 27.3 - - - +
283C VAL* 2.9 27.9 + - + +
284C GLU 3.6 4.9 - - - +
285C LEU 3.3 0.2 - - - -
286C THR* 1.3 74.5 - - - +
288C ARG* 1.3 62.4 + - - +
290C ILE* 3.1 33.9 + - + +
291C GLY 4.5 0.9 + - - -
394C CYS* 3.8 13.7 - - - -
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Residues in contact with ARG 288 (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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490B ILE 4.7 5.1 - - - -
491B GLY* 4.3 25.0 - - - -
492B VAL* 4.5 11.8 - - + +
546B ALA* 3.8 38.0 - - + +
284C GLU 3.5 7.6 + - - +
285C LEU* 3.1 44.7 + - - +
286C THR 3.0 0.4 - - - -
287C ARG* 1.3 79.4 - - - +
289C HIS* 1.3 73.8 + - + +
290C ILE 3.4 0.6 + - - -
291C GLY* 4.3 5.8 + - - -
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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