Contacts of the helix formed by residues 299 - 310 (chain J) in PDB entry 3FKS
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 299 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280J TYR* 2.7 37.9 + - - -
289J ARG* 4.6 4.7 + - - -
297J PRO* 3.5 8.1 - - - +
298J GLY* 1.3 78.0 + - - +
300J VAL* 1.3 57.8 + - - +
301J PHE 3.3 2.7 - - - -
302J TYR* 3.5 20.7 + - + +
303J LEU* 3.1 22.5 + - - +
306J ARG* 5.4 4.1 + - - -
18N GLY* 5.0 8.8 - - - -
19N ALA* 5.1 5.3 + - + +
226N PRO* 4.4 12.8 - - + -
271N LEU* 4.2 24.1 - - + +
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Residues in contact with VAL 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277J ALA* 4.3 11.4 - - + +
280J TYR* 4.7 7.0 - - + -
296J TYR* 4.1 13.7 - - + -
297J PRO* 3.5 24.4 + - + +
298J GLY 3.4 1.0 - - - -
299J ASP* 1.3 77.1 + - - +
301J PHE* 1.3 67.9 + - - +
303J LEU* 3.1 34.4 - - + +
304J HIS* 3.3 13.3 + - - +
339J TYR* 3.4 34.3 - - + +
340J ILE* 4.2 18.8 - - + -
343J ASN* 4.2 3.1 - - - +
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Residues in contact with PHE 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298J GLY 4.9 0.2 + - - -
300J VAL* 1.3 78.8 - - - +
302J TYR* 1.3 56.4 + - - +
303J LEU 3.0 4.8 + - - -
304J HIS* 3.2 6.0 + - - +
305J SER* 2.8 33.1 + - - -
339J TYR* 4.8 1.6 - - - +
343J ASN* 3.3 42.4 - - + +
346J SER* 3.7 18.6 - - - -
347J ILE* 3.5 21.7 - - + +
222N MET* 3.4 35.7 - - + -
229N ARG* 3.2 28.5 - - - -
260N ARG* 5.0 2.9 - - - -
263N GLN* 3.5 19.7 - - - +
267N GLU* 3.2 22.8 + - - +
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Residues in contact with TYR 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299J ASP* 3.7 21.7 - - + +
300J VAL 3.3 0.2 - - - -
301J PHE* 1.3 78.7 - - - +
303J LEU* 1.3 60.4 + - - +
305J SER* 3.7 7.0 - - - -
306J ARG* 3.1 62.8 + - + +
19N ALA* 5.9 3.6 - - + -
65N ASP* 5.2 0.5 + - - -
66N GLY* 4.2 17.2 + - - -
68N GLU* 4.7 3.9 + - - -
222N MET 4.7 0.2 - - - -
223N ASN 3.2 27.4 + - - -
224N GLU 3.4 5.8 - - - -
225N PRO* 3.2 43.8 - - + +
226N PRO* 4.0 13.7 - - + -
229N ARG* 3.9 13.9 - - - +
267N GLU* 4.3 1.0 + - - -
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Residues in contact with LEU 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246J TYR* 3.7 19.7 - - + -
250J PHE* 3.4 53.0 - - + -
276J GLN* 4.3 20.9 - - - +
277J ALA* 4.6 6.7 - - - -
280J TYR* 3.9 34.1 - - + -
299J ASP 3.1 12.9 + - - +
300J VAL* 3.1 22.0 - - + +
301J PHE 3.0 0.6 - - - -
302J TYR* 1.3 80.7 - - - +
304J HIS* 1.3 66.1 + - - +
305J SER 3.5 0.2 + - - -
306J ARG* 3.6 18.8 + - - +
307J LEU* 3.6 2.6 + - - +
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Residues in contact with HIS 304 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273J LEU* 3.3 46.7 + - + +
276J GLN* 3.1 28.2 + - - -
277J ALA* 3.8 19.7 - - + +
300J VAL* 3.3 12.2 + - + +
301J PHE* 3.2 6.7 + - - +
303J LEU* 1.3 81.5 - - + +
305J SER* 1.3 63.8 + - - +
307J LEU* 4.0 6.3 - - + +
308J LEU* 3.1 37.0 + - + +
340J ILE* 4.2 15.9 - - + +
343J ASN* 5.2 6.9 + - + +
344J VAL* 4.1 15.6 - - + +
347J ILE* 4.2 11.9 - - + -
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Residues in contact with SER 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301J PHE* 2.8 21.5 + - - -
302J TYR* 3.7 9.9 - - - -
303J LEU 3.2 0.2 - - - -
304J HIS* 1.3 75.8 - - - +
306J ARG* 1.3 66.3 + - - +
309J GLU* 3.3 25.6 + - - +
347J ILE* 3.9 16.6 - - - +
222N MET* 2.8 49.6 + - - +
223N ASN* 3.0 5.5 + - - +
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Residues in contact with ARG 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J GLU* 4.6 7.3 + - - -
132J GLN* 3.1 31.4 + - - +
133J VAL 5.9 1.1 - - - +
246J TYR* 4.0 11.9 + - - -
250J PHE* 3.9 11.1 - - + -
280J TYR* 5.4 4.9 + - - -
299J ASP* 5.4 4.8 + - - -
302J TYR* 3.1 64.5 + - + +
303J LEU* 3.8 31.6 - - - +
304J HIS 3.3 0.2 - - - -
305J SER* 1.3 80.4 - - - +
307J LEU* 1.3 61.8 + - - +
308J LEU 3.3 0.3 + - - -
309J GLU* 4.5 1.0 - - - +
310J ARG* 3.1 29.2 + - - +
68N GLU* 4.5 12.2 + - - -
223N ASN* 4.1 13.4 - - + +
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Residues in contact with LEU 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249J PRO* 3.2 52.9 - - + +
250J PHE* 3.6 24.4 - - + +
253J ALA* 3.7 11.8 - - + +
270J TYR* 3.3 37.3 + - + +
273J LEU* 3.8 22.4 - - + -
276J GLN* 4.6 6.1 - - - +
303J LEU 3.6 7.1 + - - +
304J HIS* 4.1 6.1 - - + +
305J SER 3.5 0.4 - - - -
306J ARG* 1.3 79.5 - - - +
308J LEU* 1.3 63.4 + - + +
310J ARG* 3.7 14.4 - - - +
311J ALA* 4.4 1.7 + - - +
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Residues in contact with LEU 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J ARG* 3.0 23.7 - - - -
270J TYR* 4.7 9.4 - - + -
273J LEU* 4.6 8.3 - - + -
304J HIS* 3.1 29.2 + - + +
305J SER 4.2 0.2 - - - +
307J LEU* 1.3 76.5 - - + +
309J GLU* 1.3 59.1 + - - +
310J ARG 2.8 11.0 + - - -
311J ALA* 2.8 17.2 + - - +
325J ALA* 4.8 4.3 - - + -
327J PRO* 3.6 30.7 - - + -
344J VAL* 4.1 12.1 - - + -
347J ILE* 3.5 40.8 - - + -
348J THR* 3.8 18.8 - - + -
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Residues in contact with GLU 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J ALA* 3.8 8.3 - - + -
141J ARG* 2.8 31.9 + - - -
166J ARG* 3.1 38.6 + - - +
305J SER* 3.3 18.6 + - - +
308J LEU* 1.3 76.6 - - - +
310J ARG* 1.3 57.9 + - - +
311J ALA 3.0 6.8 + - - +
347J ILE* 3.7 13.0 - - + +
190N ARG* 4.1 9.2 - - - +
191N THR* 3.1 37.6 + - - +
222N MET* 4.2 8.5 - - + +
223N ASN* 4.1 26.9 - - + +
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Residues in contact with ARG 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J ALA 2.8 24.8 + - - -
133J VAL* 3.4 32.3 + - - +
134J LYS 4.7 0.9 - - - +
135J ALA* 3.8 18.6 - - + +
136J PRO* 3.7 2.8 - - - +
250J PHE* 3.7 22.5 + - - -
253J ALA* 3.3 12.1 - - + +
254J SER* 2.8 37.8 + - - +
257J GLU* 2.7 29.1 + - - +
260J ARG* 2.8 29.8 + - - +
306J ARG* 3.1 25.7 + - - +
307J LEU* 3.7 13.7 - - - +
308J LEU 2.8 0.6 + - - -
309J GLU* 1.3 77.3 - - - +
311J ALA* 1.3 58.2 + - - +
323J LEU* 4.3 7.3 - - + +
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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