Contacts of the helix formed by residues 316 - 334 (chain D) in PDB entry 1FP1
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 SER 316 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D ASN* 2.6 26.5 + - - +
315D THR* 1.3 83.1 - - - +
317D GLU* 1.3 60.4 + - - +
318D GLU* 3.0 37.4 + - - +
319D SER* 3.2 2.1 + - - -
320D LYS* 3.0 27.7 + - - +
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Residues in contact with GLU 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D THR 5.3 0.3 - - - +
316D SER* 1.3 71.1 - - - +
318D GLU* 1.3 66.5 + - - +
320D LYS* 3.2 19.0 + - + +
321D LEU* 2.8 31.2 + - + +
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Residues in contact with GLU 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D ILE 5.8 0.9 - - - +
310D PRO* 4.6 12.3 - - + -
314D ASN* 5.1 1.0 - - - +
316D SER* 3.0 29.6 + - - +
317D GLU* 1.3 82.6 + - - +
319D SER* 1.3 57.9 + - - +
321D LEU* 4.5 3.4 - - - -
322D VAL* 2.9 37.4 + - + +
362D PHE 5.2 0.9 - - - +
363D ASN* 3.5 35.5 - - + +
364D SER* 3.9 14.4 - - - -
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Residues in contact with SER 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D PRO* 3.8 20.4 - - - +
313D PRO* 3.7 10.6 - - - +
314D ASN* 3.0 56.8 + - - -
316D SER* 3.2 2.5 + - - -
318D GLU* 1.3 78.5 - - - +
320D LYS* 1.3 67.2 + - - +
323D SER* 3.1 32.6 + - - -
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Residues in contact with LYS 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D ASN 4.8 2.2 + - - +
315D THR* 2.8 37.3 + - - +
316D SER 3.0 12.4 + - - +
317D GLU* 3.4 21.7 + - + +
319D SER* 1.3 77.2 - - - +
321D LEU* 1.3 56.5 + - - +
323D SER* 3.9 2.1 - - - -
324D THR* 2.8 35.2 + - - +
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Residues in contact with LEU 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D PHE* 3.6 31.2 - - + -
317D GLU 2.8 19.9 + - - +
318D GLU* 3.8 4.9 - - - +
319D SER 3.2 0.2 - - - -
320D LYS* 1.3 70.7 - - - +
322D VAL* 1.3 68.3 + - - +
324D THR* 3.0 11.4 + - + -
325D LEU* 2.9 43.1 + - + +
362D PHE* 5.9 2.5 - - + -
364D SER* 3.9 11.7 - - - +
2000D HCC 4.9 11.7 - - + +
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Residues in contact with VAL 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D PHE* 3.9 27.1 - - + -
308D ILE 3.7 15.9 - - - +
309D LEU* 3.5 42.2 - - + +
310D PRO* 4.5 1.6 - - + -
318D GLU* 2.9 21.1 + - + +
321D LEU* 1.3 73.3 - - + +
323D SER* 1.3 57.7 + - - +
325D LEU* 3.3 6.8 + - - +
326D ASP* 2.8 27.5 + - - +
337D GLU* 3.7 13.9 - - + +
364D SER* 4.2 15.3 - - - -
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Residues in contact with SER 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D LEU* 3.7 14.9 - - - +
313D PRO* 5.4 6.8 - - - +
319D SER* 3.1 24.9 + - - -
320D LYS* 4.1 2.7 - - - -
322D VAL* 1.3 77.8 - - - +
324D THR* 1.3 61.0 + - - +
326D ASP* 3.5 8.9 + - - +
327D ASN* 2.9 36.6 + - - -
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Residues in contact with THR 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LEU* 6.5 1.3 - - + -
320D LYS* 2.8 24.8 + - - +
321D LEU* 3.3 11.7 - - + -
323D SER* 1.3 77.9 - - - +
325D LEU* 1.3 65.2 + - + +
327D ASN* 3.3 7.1 + - - +
328D LEU* 2.9 30.1 + - + +
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Residues in contact with LEU 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D PHE* 5.7 0.4 - - + -
307D PHE* 3.6 43.5 - - + -
321D LEU* 2.9 34.3 + - + +
322D VAL* 3.7 6.7 - - - +
324D THR* 1.3 75.9 - - + +
326D ASP* 1.3 56.6 + - - +
328D LEU* 3.0 15.6 + - + +
329D MET* 2.7 40.4 + - + +
337D GLU* 4.0 15.3 - - + +
2000D HCC 3.7 43.7 - - + -
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Residues in contact with ASP 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D LEU* 4.2 12.8 - - + +
322D VAL 2.8 18.9 + - - +
323D SER* 3.5 11.5 + - - +
325D LEU* 1.3 76.5 - - - +
327D ASN* 1.3 60.3 + - - +
329D MET* 3.3 2.5 + - - +
330D PHE* 3.0 29.0 + - - +
336D ARG* 3.4 10.2 - - - +
337D GLU* 2.8 44.5 + - + +
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Residues in contact with ASN 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D PHE* 3.4 35.0 - - + -
323D SER* 2.9 33.5 + - - +
324D THR* 3.7 5.7 - - - +
326D ASP* 1.3 77.5 + - - +
328D LEU* 1.3 65.5 + - - +
330D PHE* 3.8 7.2 - - - +
331D ILE* 3.1 25.5 + - - +
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Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D PHE* 3.7 21.1 - - + -
138D PHE* 5.4 0.2 - - + -
139D LEU* 3.9 13.9 - - + -
148D TRP* 3.5 33.2 - - + -
324D THR* 2.9 17.1 + - + +
325D LEU* 3.3 25.8 - - + +
327D ASN* 1.3 79.1 - - - +
329D MET* 1.3 58.2 + - - +
331D ILE* 3.4 5.4 - - - +
332D THR* 2.8 33.2 + - - +
2000D HCC 3.6 37.0 - - + -
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Residues in contact with MET 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D HIS* 3.6 34.3 - - + +
279D ASN* 3.2 26.9 - - - +
325D LEU* 2.7 24.1 + - + +
326D ASP 3.7 4.5 - - - +
328D LEU* 1.3 72.0 - - - +
330D PHE* 1.3 66.1 + - - +
332D THR* 3.0 5.1 - - - +
333D VAL* 2.9 40.5 + - + +
334D GLY 3.0 5.5 + - - -
335D GLY 3.1 17.5 + - - -
336D ARG* 3.8 4.0 - - - +
337D GLU* 3.3 21.1 - - - +
2000D HCC 4.1 28.9 - - + +
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Residues in contact with PHE 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D PHE* 3.8 29.4 - + - -
154D ALA* 3.2 47.3 - - + -
155D VAL* 3.9 16.4 - - + -
326D ASP* 3.0 17.5 + - - +
327D ASN* 3.8 5.8 - - - +
328D LEU 3.4 0.2 - - - -
329D MET* 1.3 75.5 - - - +
331D ILE* 1.3 68.8 + - + +
334D GLY* 2.9 29.6 + - - -
335D GLY 3.5 15.8 + - - +
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Residues in contact with ILE 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D VAL* 3.5 43.9 - - + +
148D TRP* 3.5 25.4 - - + -
150D ASN 5.3 0.2 - - - -
151D PHE* 3.5 41.1 - - + -
154D ALA* 4.6 14.0 - - + +
327D ASN 3.1 16.6 + - - +
328D LEU* 3.4 8.5 - - - +
330D PHE* 1.3 87.6 - - + +
332D THR* 1.3 64.2 + - - +
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Residues in contact with THR 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D PHE* 5.6 1.2 - - - -
148D TRP* 5.1 6.8 - - - -
328D LEU* 2.8 31.4 + - - +
329D MET* 3.0 18.4 - - - +
331D ILE* 1.3 81.9 - - - +
333D VAL* 1.3 87.4 + - + +
334D GLY 3.7 0.2 - - - -
2000D HCC 2.6 36.6 + - + +
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Residues in contact with VAL 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D ASN* 3.9 17.2 - - + +
329D MET* 2.9 26.9 + - + +
332D THR* 1.3 97.5 - - + +
334D GLY* 1.3 62.7 + - - +
335D GLY* 3.4 15.9 - - - +
2000D HCC 4.4 11.7 - - + +
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Residues in contact with GLY 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ASN 4.8 3.2 - - - +
280D TRP 5.9 0.5 - - - -
330D PHE* 2.9 26.6 + - - -
332D THR 3.7 0.4 - - - -
333D VAL* 1.3 78.9 - - - +
335D GLY* 1.3 64.3 + - - +
336D ARG* 4.1 15.4 + - - -
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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
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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