Contacts of the helix formed by residues 277 - 287 (chain P) in PDB entry 6FF7
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 ARG 277 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229P LYS* 3.6 40.0 - - + +
231P ILE 5.2 5.6 - - - +
232P THR* 5.1 11.4 - - - -
274P PHE* 4.4 11.6 - - - +
275P ALA 4.0 2.1 + - - -
276P THR* 1.3 69.5 - - - +
278P GLN* 1.3 50.8 + - - +
279P ALA 2.9 0.5 + - - -
280P ALA* 2.9 35.9 + - + +
281P GLU* 3.2 10.9 + - + +
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Residues in contact with GLN 278 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276P THR 2.7 11.7 + - - +
277P ARG* 1.3 70.9 - - - +
279P ALA* 1.3 56.8 + - - +
281P GLU* 2.9 30.8 + - + +
282P VAL* 3.2 8.0 + - - +
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Residues in contact with ALA 279 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255P PHE* 3.4 41.0 - - + +
256P GLY* 5.3 1.1 - - - -
274P PHE* 5.6 4.9 - - + -
276P THR 4.1 4.2 + - - +
277P ARG 2.9 3.8 + - - +
278P GLN* 1.3 74.6 - - - +
280P ALA* 1.3 63.1 + - - +
282P VAL* 3.0 17.1 + - - +
283P ALA* 3.2 8.7 + - - +
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Residues in contact with ALA 280 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232P THR* 5.0 14.1 - - - +
255P PHE* 5.2 1.7 - - - +
273P GLN 5.5 1.1 - - - -
274P PHE* 4.0 20.2 - - + +
277P ARG* 2.9 11.5 + - + +
279P ALA* 1.3 77.1 - - - +
281P GLU* 1.3 49.8 + - - +
283P ALA* 3.0 15.1 + - + +
284P ALA* 2.8 31.4 + - - +
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Residues in contact with GLU 281 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277P ARG* 3.2 8.8 + - + +
278P GLN* 2.9 27.1 + - - +
280P ALA* 1.3 76.1 - - - +
282P VAL* 1.3 55.5 + - - +
284P ALA* 2.9 14.3 + - - +
285P GLU* 2.9 21.7 + - - +
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Residues in contact with VAL 282 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278P GLN 3.2 7.7 + - - +
279P ALA* 3.0 11.4 + - - +
281P GLU* 1.3 73.3 - - - +
283P ALA* 1.3 54.7 + - - +
285P GLU* 2.9 14.1 + - + +
286P LYS* 2.6 34.1 + - - +
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Residues in contact with ALA 283 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255P PHE* 5.9 5.2 - - + -
279P ALA 3.2 5.9 + - - +
280P ALA* 3.0 24.4 + - + +
282P VAL* 1.3 77.6 - - - +
284P ALA* 1.3 50.7 + - - +
286P LYS* 3.4 9.4 - - + -
287P SER* 2.7 40.6 + - - -
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Residues in contact with ALA 284 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280P ALA 2.8 11.1 + - - +
281P GLU* 3.1 15.5 - - - +
283P ALA* 1.3 76.1 - - - +
285P GLU* 1.3 58.5 + - - +
287P SER* 4.0 6.5 + - - +
288P PHE* 4.0 17.2 + - - +
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Residues in contact with GLU 285 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281P GLU 2.9 6.9 + - - +
282P VAL* 2.9 21.3 + - + +
284P ALA* 1.3 77.4 - - - +
286P LYS* 1.3 60.0 + - - +
288P PHE* 4.6 4.4 + - - +
290P LYS* 4.8 4.9 - - - +
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Residues in contact with LYS 286 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282P VAL 2.6 17.5 + - - +
283P ALA* 2.9 11.6 + - + +
285P GLU* 1.3 76.7 - - - +
287P SER* 1.3 59.0 + - - +
288P PHE 3.7 0.7 - - - -
290P LYS* 3.3 9.8 - - - +
291P LEU* 2.9 28.3 + - + -
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Residues in contact with SER 287 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283P ALA* 2.7 20.3 + - - -
284P ALA* 4.4 4.4 - - - -
285P GLU 3.5 0.2 - - - -
286P LYS* 1.3 75.8 - - - +
288P PHE* 1.3 57.3 + - - +
289P ASN 3.4 3.0 + - - -
291P LEU* 3.8 20.0 - - - +
300P VAL* 3.3 28.9 - - - +
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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