Contacts of the helix formed by residues 242 - 262 (chain B) in PDB entry 5FN3
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 PRO 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLY 6.0 0.9 - - - +
117B PRO* 4.8 20.4 - - + +
119B THR* 5.8 6.7 - - - +
132B SER* 6.0 0.4 - - - -
135B ASN* 5.1 1.3 - - - +
240B TYR 4.3 3.6 - - - +
241B LEU* 1.4 80.3 - - + +
243B GLU* 1.3 55.8 + - - +
244B TRP* 3.1 2.7 - - + +
245B THR* 2.6 64.7 + - + +
246B ALA 3.1 3.3 + - - -
395B LYS* 4.1 0.7 - - - +
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Residues in contact with GLU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PRO* 1.3 71.9 - - - +
244B TRP* 1.3 71.9 + - + +
246B ALA* 3.2 8.5 + - - +
247B TRP* 2.9 33.6 - - - +
395B LYS* 3.5 24.8 - - + +
399B THR* 5.3 17.5 - - + +
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Residues in contact with TRP 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 5.3 3.2 + - - +
128B ARG* 5.6 1.8 - - + -
129B ALA* 4.3 30.3 - - + +
132B SER* 4.2 13.7 - - - +
242B PRO* 2.9 1.5 + - + -
243B GLU* 1.3 91.5 - - + +
245B THR* 1.3 61.6 + - - +
246B ALA 3.4 0.5 + - - -
247B TRP* 3.7 12.5 + + + +
248B LEU* 3.3 31.0 + - + +
447B PHE* 5.4 10.3 - + - -
451B TYR* 4.1 19.3 - - - -
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Residues in contact with THR 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO* 4.8 4.5 - - + -
132B SER* 4.0 6.7 - - - -
135B ASN* 3.1 35.3 + - - +
136B ALA* 4.2 14.2 - - + +
139B MET* 6.2 0.2 - - + -
241B LEU* 5.0 5.8 - - + -
242B PRO* 2.6 44.5 + - + +
244B TRP* 1.3 73.8 - - - +
246B ALA* 1.3 56.5 + - - +
248B LEU* 3.3 11.2 + - - +
249B ILE* 2.9 39.0 + - + +
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 4.3 23.1 - - + +
242B PRO 3.1 3.2 + - - +
243B GLU 3.2 10.9 + - - +
245B THR* 1.3 79.6 - - - +
247B TRP* 1.3 58.7 + - + +
249B ILE* 3.1 7.7 - - - +
250B LEU* 2.9 35.0 + - + +
391B VAL* 5.6 3.1 - - + -
395B LYS* 3.7 36.3 - - + -
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Residues in contact with TRP 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLU* 2.9 33.7 + - + +
244B TRP* 4.3 12.7 - + + +
245B THR 3.5 0.2 - - - -
246B ALA* 1.3 75.2 - - + +
248B LEU* 1.3 58.2 + - + +
250B LEU* 3.2 12.6 + - + +
251B ALA* 2.9 29.2 + - - +
392B LEU* 3.6 26.9 - - + -
395B LYS* 3.6 31.9 - - + +
396B ALA* 4.2 0.9 - - + -
443B LEU* 3.6 36.3 - - + +
446B TYR* 3.0 58.8 + + + -
447B PHE* 3.7 33.0 - + + -
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA* 4.8 0.7 - - + +
132B SER* 3.2 28.5 - - - +
133B ILE* 3.9 37.7 - - + -
136B ALA* 4.9 7.6 - - + -
244B TRP* 3.3 19.0 + - + +
245B THR* 3.3 7.6 + - - +
246B ALA 3.2 0.2 - - - -
247B TRP* 1.3 78.9 - - + +
249B ILE* 1.3 57.6 + - - +
251B ALA* 3.2 9.0 + - + +
252B VAL* 2.9 36.2 + - + +
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA* 4.6 8.7 - - + +
139B MET* 4.0 31.9 - - + -
140B ILE* 4.5 17.0 - - + -
143B ILE* 4.4 13.9 - - + -
241B LEU* 4.5 18.8 - - + -
245B THR* 2.9 26.8 + - + +
246B ALA* 3.1 15.0 + - - +
248B LEU* 1.3 76.9 - - - +
250B LEU* 1.3 64.0 - - + +
252B VAL* 3.2 7.4 + - - +
253B ILE* 2.9 46.3 + - + +
388B PHE* 4.6 7.0 - - + -
391B VAL* 6.6 0.2 - - + -
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ALA* 2.9 22.3 + - + +
247B TRP* 3.3 34.1 - - + +
249B ILE* 1.3 79.1 - - + +
251B ALA* 1.3 53.1 + - - +
253B ILE* 3.2 9.4 + - + +
254B SER* 2.7 36.1 + - - -
388B PHE* 3.6 48.0 - - + +
391B VAL* 4.9 9.9 - - + -
392B LEU* 4.3 17.7 - - + +
395B LYS* 5.8 1.1 - - + -
439B ILE* 4.1 17.1 - - + +
443B LEU* 4.1 14.6 - - + -
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B TRP 2.9 12.8 + - - +
248B LEU* 3.3 13.7 - - + +
250B LEU* 1.3 75.9 - - - +
252B VAL* 1.3 58.5 + - + +
254B SER* 2.7 19.7 + - - -
255B VAL* 2.9 27.8 + - + +
443B LEU* 4.3 12.7 - - + +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE* 6.0 5.6 - - + -
136B ALA* 5.9 0.4 - - + -
140B ILE* 3.6 52.3 - - + -
248B LEU* 2.9 23.0 + - + +
249B ILE 3.2 8.7 + - - +
251B ALA* 1.3 77.2 - - + +
253B ILE* 1.3 53.7 + - + +
255B VAL* 2.9 17.2 - - + +
256B THR* 2.8 43.7 + - + +
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Residues in contact with ILE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE* 6.5 0.4 - - + -
143B ILE* 5.1 17.3 - - + -
249B ILE* 2.9 37.3 + - + +
250B LEU* 3.4 9.6 - - + +
252B VAL* 1.3 77.1 - - + +
254B SER* 1.3 59.3 + - - +
256B THR* 2.5 32.9 + - + +
257B ASP* 2.9 17.9 + - - +
385B ASP* 4.7 13.7 - - - +
388B PHE* 3.3 57.7 - - + -
439B ILE* 4.9 4.7 - - + -
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Residues in contact with SER 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B LEU 2.7 24.0 + - - -
251B ALA* 2.7 16.5 + - - -
253B ILE* 1.3 76.9 - - - +
255B VAL* 1.3 62.3 + - - +
258B LEU* 3.2 14.0 + - - +
436B PRO* 3.0 51.3 - - - +
439B ILE* 3.9 12.6 - - - +
440B THR* 3.8 10.8 + - - -
443B LEU* 4.9 1.6 - - - +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ALA* 2.9 20.2 + - + +
252B VAL* 2.9 33.2 - - + +
254B SER* 1.3 77.3 - - - +
256B THR* 1.3 60.5 + - + +
258B LEU* 3.2 9.0 + - - +
259B VAL* 2.9 39.2 + - + +
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Residues in contact with THR 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ILE* 5.2 6.7 - - + -
144B VAL* 5.6 8.1 - - + -
252B VAL* 2.8 40.2 + - + +
253B ILE* 2.5 20.4 + - + +
255B VAL* 1.3 79.8 - - + +
257B ASP* 1.3 77.0 + - - +
259B VAL* 3.2 8.9 + - - +
260B ALA* 2.9 29.0 + - - +
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Residues in contact with ASP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B ILE* 2.9 16.3 + - + +
256B THR* 1.3 88.8 + - - +
258B LEU* 1.3 55.0 - - - +
260B ALA* 3.2 12.1 + - - +
261B VAL* 2.9 40.8 + - - +
385B ASP* 3.5 24.2 - - - +
432B LEU 4.9 6.2 - - - +
433B PRO 5.0 0.6 - - - +
435B LEU* 5.5 2.1 - - - +
436B PRO* 4.2 21.5 - - + -
28G ALA* 4.6 17.2 - - - +
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Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B SER 3.2 13.1 + - - +
255B VAL* 3.2 12.7 + - - +
257B ASP* 1.3 76.9 - - - +
259B VAL* 1.3 63.3 + - + +
261B VAL* 3.2 25.0 + - + +
262B LEU* 3.2 28.4 + - + +
433B PRO* 5.1 2.9 - - + +
434B ALA* 6.2 0.9 - - - -
436B PRO* 4.1 16.5 - - + +
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Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B VAL* 2.9 25.7 + - + +
256B THR* 3.2 10.1 + - - +
258B LEU* 1.3 74.4 - - + +
260B ALA* 1.3 65.3 + - - +
262B LEU* 3.1 14.3 + - - -
263B CYS* 3.5 32.1 - - + +
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Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR 2.9 12.7 + - - +
257B ASP* 3.2 17.2 + - - +
259B VAL* 1.3 79.6 - - - +
261B VAL* 1.3 63.1 + - + +
262B LEU 3.3 6.4 + - - +
263B CYS* 4.7 5.2 + - - -
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASP* 2.9 24.1 + - - +
258B LEU* 3.2 17.7 + - + +
260B ALA* 1.3 76.9 - - + +
262B LEU* 1.3 74.8 + - + +
430B LYS* 4.3 24.3 + - + +
431B ALA 4.8 5.6 - - - +
432B LEU 4.9 0.4 - - - +
433B PRO* 3.4 50.7 - - + +
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 3.2 23.7 + - + +
259B VAL* 3.1 9.9 + - - +
260B ALA 3.9 5.4 - - - +
261B VAL* 1.3 94.5 - - + +
263B CYS* 1.4 71.3 + - - +
430B LYS* 6.5 0.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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