Contacts of the helix formed by residues 264 - 276 (chain B) in PDB entry 5FN2
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 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B THR* 5.1 10.8 - - + +
148B ILE* 5.9 5.8 - - + -
151B VAL* 3.9 19.8 - - + +
259B VAL* 3.8 4.7 - - + +
260B ALA* 2.5 42.8 - - + +
263B CYS* 1.4 80.3 - - + +
265B LYS* 1.3 58.9 + - + +
267B PRO* 2.3 41.9 - - + +
268B LEU 2.8 3.3 + - - -
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Residues in contact with LYS 265 (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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147B THR* 5.7 3.8 - - - +
150B LEU* 6.1 1.8 - - + -
151B VAL* 5.0 3.7 - - + +
257B ASP* 3.5 15.5 - - - +
260B ALA* 3.1 22.7 - - + +
261B VAL* 2.7 44.6 + - - +
264B PRO* 1.3 78.3 - - + +
266B GLY* 1.3 68.0 + - - +
267B PRO 2.9 0.7 - - - -
268B LEU* 2.5 37.0 + - + -
269B ARG* 2.5 18.4 + - - +
431B ALA* 2.6 31.5 + - + +
432B LEU* 4.4 6.5 + - - +
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Residues in contact with GLY 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B VAL 3.6 12.7 + - - -
262B LEU 4.6 2.7 - - - -
263B CYS* 1.9 25.2 + - - -
265B LYS* 1.3 78.7 - - - +
267B PRO* 1.4 55.0 - - - +
269B ARG* 4.1 2.1 - - - +
270B MET* 2.9 32.6 + - - +
431B ALA* 4.5 10.5 - - - +
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Residues in contact with PRO 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 4.8 6.7 - - + -
262B LEU 4.9 0.4 - - - +
263B CYS* 2.2 41.2 - - + +
264B PRO* 2.3 27.0 - - + +
266B GLY* 1.4 69.0 - - - +
268B LEU* 1.3 52.5 + - - +
270B MET* 3.3 19.6 - - + +
271B LEU* 2.9 34.0 + - - +
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Residues in contact with LEU 268 (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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150B LEU* 4.4 15.0 - - + -
151B VAL* 4.2 16.8 - - + +
154B TYR* 3.3 42.0 - - + -
264B PRO 2.8 6.4 + - - +
265B LYS* 2.5 34.2 + - + +
267B PRO* 1.3 72.6 - - - +
269B ARG* 1.3 80.7 + - + +
271B LEU* 3.2 6.6 + - - +
272B VAL* 2.9 35.2 + - + +
279B ASN 5.1 3.1 - - - +
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Residues in contact with ARG 269 (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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265B LYS* 2.5 22.8 + - + +
266B GLY* 4.1 3.8 - - - +
268B LEU* 1.3 86.7 - - + +
270B MET* 1.3 57.5 + - - +
272B VAL* 3.2 9.3 + - + +
273B GLU* 2.9 47.7 + - + +
380B LYS* 3.8 38.4 + - - +
425B LEU* 4.5 13.9 - - - +
429B LYS 6.2 0.2 - - - -
430B LYS 4.8 4.2 + - - -
431B ALA* 3.5 19.6 - - + +
432B LEU* 3.3 45.3 - - - +
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Residues in contact with MET 270 (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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266B GLY 2.9 24.7 + - - +
267B PRO* 3.3 26.5 - - + +
269B ARG* 1.3 78.3 - - - +
271B LEU* 1.3 75.6 + - + +
273B GLU* 3.2 16.2 + - - +
274B THR* 2.7 43.2 + - - -
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Residues in contact with LEU 271 (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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154B TYR* 3.6 54.5 - - + +
155B LYS* 5.3 4.9 - - - +
267B PRO 2.9 22.8 + - - +
268B LEU* 3.3 4.3 - - - +
270B MET* 1.3 92.6 - - + +
272B VAL* 1.3 60.9 + - - +
274B THR* 3.2 9.9 + - - -
275B ALA* 2.9 35.8 + - + +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TYR* 3.6 22.0 - - + -
268B LEU* 2.9 28.9 + - + +
269B ARG* 3.3 12.3 - - + +
271B LEU* 1.3 80.9 - - - +
273B GLU* 1.3 61.6 + - + +
275B ALA* 3.2 3.0 + - - -
276B GLN 2.9 35.3 + - - +
277B GLU 3.2 16.2 - - - +
278B ARG* 3.8 13.2 - - - -
279B ASN* 3.0 33.9 - - - +
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Residues in contact with GLU 273 (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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269B ARG* 2.9 31.5 + - + +
270B MET* 3.4 15.5 - - - +
272B VAL* 1.3 82.2 - - + +
274B THR* 1.3 62.7 + - - +
275B ALA 4.3 0.2 - - - -
276B GLN* 4.0 10.7 + - - +
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Residues in contact with THR 274 (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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270B MET* 2.7 30.4 + - - -
271B LEU* 3.2 13.6 + - - -
273B GLU* 1.3 77.0 - - - +
275B ALA* 1.3 63.4 - - - +
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Residues in contact with ALA 275 (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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271B LEU* 2.9 26.1 + - + +
272B VAL* 3.2 5.4 + - - +
273B GLU 4.3 0.4 - - - -
274B THR* 1.3 81.0 - - - +
276B GLN* 1.3 66.8 + - + +
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Residues in contact with GLN 276 (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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272B VAL 2.9 19.2 + - - +
273B GLU* 4.0 9.1 + - - +
274B THR 3.8 0.4 - - - -
275B ALA* 1.3 80.2 - - + +
277B GLU* 1.3 67.4 + - + +
278B ARG 4.0 0.2 + - - -
279B ASN* 6.0 2.2 - - - +
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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