Contacts of the helix formed by residues 316 - 333 (chain A) in PDB entry 1FPQ
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ASN* 2.6 31.2 + - - +
315A THR* 1.3 76.0 - - - +
317A GLU* 1.3 63.9 + - - +
318A GLU* 2.9 40.1 + - - +
319A SER* 3.2 3.3 + - - -
320A LYS* 3.1 22.5 + - - +
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Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER 5.9 0.2 - - - +
26A LEU* 3.4 21.5 - - + -
27A SER* 4.2 18.2 - - - +
30A VAL* 3.8 26.2 - - + +
315A THR 4.7 1.6 - - - +
316A SER* 1.3 75.0 - - - +
318A GLU* 1.3 58.5 + - - +
320A LYS* 3.3 34.8 + - - +
321A LEU* 2.8 29.8 + - - +
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.7 23.7 - - + +
308A ILE 5.8 1.3 - - - +
310A PRO* 5.0 10.1 - - + -
314A ASN* 4.8 0.6 + - - +
316A SER* 2.9 34.0 + - - +
317A GLU* 1.3 76.3 + - - +
319A SER* 1.3 61.4 + - - +
322A VAL* 2.9 37.8 + - + +
360A ARG* 5.9 2.9 - - - +
363A ASN* 3.4 30.9 - - - +
364A SER* 3.8 11.9 - - - -
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 5.1 0.2 + - - -
94A SER* 2.7 22.3 + - - -
310A PRO* 3.8 18.7 - - - +
313A PRO* 3.8 6.8 - - - +
314A ASN* 3.0 49.6 + - - -
316A SER* 3.2 7.5 + - - -
318A GLU* 1.3 76.9 - - - +
320A LYS* 1.3 63.7 + - - +
323A SER* 3.1 31.2 + - - -
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Residues in contact with LYS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.6 7.9 - - + -
91A LEU* 4.0 2.4 - - - +
94A SER* 3.3 33.7 - - - +
95A TYR* 3.9 45.6 - - + +
315A THR* 3.7 18.5 + - - -
316A SER 3.1 14.3 + - - +
317A GLU* 3.5 34.8 + - - +
319A SER* 1.3 77.5 - - - +
321A LEU* 1.3 60.6 + - - +
323A SER 4.0 0.3 - - - -
324A THR* 2.8 30.5 + - - -
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.5 26.2 - - + -
29A MSE 3.7 43.1 - - + +
30A VAL* 4.0 7.8 - - + +
33A THR* 4.0 11.9 - - + +
307A PHE* 3.8 30.5 - - + -
317A GLU 2.8 17.3 + - - +
318A GLU 3.8 3.1 - - - +
319A SER 3.3 0.2 - - - -
320A LYS* 1.3 76.3 - - - +
322A VAL* 1.3 65.1 + - - +
324A THR* 2.9 15.8 + - - -
325A LEU* 2.9 29.7 + - + +
364A SER* 3.9 4.5 - - - +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PHE* 4.1 23.3 - - + -
308A ILE 3.6 18.2 - - - +
309A LEU* 3.6 40.2 - - + +
310A PRO* 4.7 1.8 - - + -
318A GLU* 2.9 21.4 + - + +
321A LEU* 1.3 73.0 - - + +
323A SER* 1.3 57.3 + - - +
325A LEU* 3.4 7.0 + - - +
326A ASP* 3.0 27.5 + - - +
337A GLU* 4.0 14.4 - - + -
364A SER* 4.2 17.3 - - - -
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG 5.1 0.9 - - - -
90A ARG* 3.6 26.5 + - - +
91A LEU* 3.9 26.2 - - - -
94A SER* 4.0 3.3 + - - -
309A LEU* 3.9 12.7 - - - +
319A SER* 3.1 23.4 + - - -
320A LYS 4.1 0.9 - - - -
322A VAL* 1.3 78.4 - - - +
324A THR* 1.3 57.0 + - - +
326A ASP* 3.5 7.4 + - - +
327A ASN* 2.7 35.6 + - - -
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Residues in contact with THR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 6.0 0.7 - - - +
33A THR* 3.7 29.1 + - - +
36A VAL* 3.4 38.4 - - + +
37A TYR* 5.3 2.9 + - - +
91A LEU* 3.7 18.6 - - - +
95A TYR* 4.7 6.6 + - - -
320A LYS 2.8 18.0 + - - -
321A LEU* 2.9 12.8 + - - -
323A SER* 1.3 75.8 - - - +
325A LEU* 1.3 61.3 + - + +
327A ASN 3.3 1.7 + - - -
328A LEU* 3.0 26.6 + - + +
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Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 4.6 17.0 - - + -
307A PHE* 3.5 50.0 - - + -
321A LEU* 2.9 29.3 + - + +
322A VAL* 3.8 7.0 - - - +
324A THR* 1.3 76.5 - - - +
326A ASP* 1.3 53.7 + - - +
328A LEU* 3.0 20.8 + - + +
329A MSE 2.7 45.7 + - + +
337A GLU* 4.2 14.1 - - + +
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Residues in contact with ASP 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 2.9 69.8 + - - +
90A ARG* 5.4 3.1 - - - -
309A LEU* 4.5 11.5 - - + +
322A VAL 3.0 18.1 + - - +
323A SER* 3.5 10.7 - - - +
325A LEU* 1.3 77.4 - - - +
327A ASN* 1.3 59.1 + - - +
329A MSE 3.4 2.0 + - - +
330A PHE 3.1 9.0 + - - -
336A ARG* 3.3 2.6 - - - +
337A GLU* 2.7 44.4 + - + +
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Residues in contact with ASN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.9 17.0 - - + -
40A VAL* 3.9 15.5 - - + +
87A ARG* 3.1 26.6 + - - +
88A MSE 3.7 27.9 + - - +
91A LEU* 3.8 12.5 - - - +
323A SER 2.7 25.8 + - - +
324A THR 3.7 5.8 - - - +
325A LEU 3.2 0.2 - - - -
326A ASP* 1.3 77.6 - - - +
328A LEU* 1.3 66.1 + - - +
330A PHE* 3.6 13.0 + - + +
331A ILE* 3.2 26.4 + - - +
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 5.1 11.2 - - + -
36A VAL* 4.1 24.4 - - + +
324A THR* 3.0 12.9 + - + +
325A LEU* 3.3 24.5 - - + +
327A ASN* 1.3 76.9 - - - +
329A MSE 1.3 86.0 + - + +
331A ILE* 3.2 9.0 - - + +
332A THR* 3.0 41.1 + - + +
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Residues in contact with MSE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A HIS* 3.3 31.2 - - + +
279A ASN* 4.9 5.8 - - - +
325A LEU* 2.7 27.3 + - + +
326A ASP 3.7 4.7 - - - +
328A LEU* 1.3 105.9 - - + +
330A PHE* 1.3 50.6 + - - +
332A THR* 4.6 5.2 - - + -
333A VAL* 2.5 49.9 + - - +
335A GLY* 3.8 19.3 - - - -
336A ARG* 4.1 2.2 - - - +
337A GLU* 3.3 24.2 - - - +
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ARG* 3.7 51.1 - - + -
87A ARG* 3.3 37.2 - - + +
88A MSE 6.4 2.5 - - + -
326A ASP 3.1 7.9 + - - +
327A ASN* 3.7 14.1 - - - +
329A MSE 1.3 78.1 - - - +
331A ILE* 1.3 84.0 + - + +
333A VAL 2.4 26.8 + - - +
334A GLY* 6.0 2.5 - - - -
335A GLY 3.6 6.0 + - - -
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 6.2 3.8 - - + -
327A ASN 3.2 12.0 + - - +
328A LEU* 3.2 17.7 - - + +
330A PHE* 1.3 94.3 - - + +
332A THR* 1.3 69.3 + - - +
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Residues in contact with THR 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A PHE* 6.3 2.7 - - + -
328A LEU* 3.0 34.7 + - + +
329A MSE 3.9 5.4 - - + -
331A ILE* 1.3 84.3 - - - +
333A VAL* 1.3 78.8 + - + +
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Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASN* 4.9 20.4 - - + +
329A MSE 2.5 24.1 + - + +
330A PHE* 2.4 29.5 + - - +
332A THR* 1.3 97.5 - - + +
334A GLY* 1.3 71.8 + - - +
335A GLY* 2.9 12.2 + - - +
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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