Contacts of the helix formed by residues 340 - 354 (chain E) in PDB entry 3SRF
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 THR 340 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332E SER* 3.6 23.1 - - - +
339E PRO* 1.3 79.7 - - - +
341E ARG* 1.3 65.2 + - - +
342E ALA* 3.4 8.7 + - - +
343E GLU* 2.9 37.8 + - - +
344E GLY* 3.2 17.8 + - - -
328F GLN* 3.2 22.0 - - - +
331F GLU* 4.4 20.4 - - + -
343F GLU* 4.5 5.3 + - - +
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Residues in contact with ARG 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E ARG* 5.1 5.0 - - - +
339E PRO 3.7 16.8 + - - -
340E THR* 1.3 72.2 - - - +
342E ALA* 1.3 63.3 + - - +
344E GLY* 3.7 2.5 - - - +
345E SER* 3.2 18.0 + - - -
177F ASP* 3.7 13.3 + - - -
293F ARG* 2.8 68.6 + - + +
294F GLY* 2.6 28.4 + - - +
297F GLY* 3.3 27.7 + - - -
298F ILE* 3.4 11.1 - - - +
302F ALA* 5.5 9.9 - - - +
305F VAL* 4.9 11.6 - - + +
327F THR* 4.2 4.7 - - + +
328F GLN* 3.0 32.0 + - + +
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Residues in contact with ALA 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340E THR* 3.2 2.9 + - - +
341E ARG* 1.3 78.2 - - - +
343E GLU* 1.3 59.9 - - - +
345E SER* 3.4 3.8 + - - -
346E ASP* 3.2 16.8 + - - +
293F ARG* 3.6 0.2 - - - +
328F GLN 3.1 23.8 + - - +
329F MET 3.8 1.3 - - - +
342F ALA 3.3 13.7 - - - +
343F GLU* 3.6 27.6 - - + -
346F ASP* 3.4 27.5 - - + +
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Residues in contact with GLU 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E GLN 4.6 0.9 - - - +
329E MET 3.2 18.5 - - - +
330E LEU* 3.8 13.1 - - + +
331E GLU* 3.7 11.6 + - - +
332E SER* 2.5 51.1 + - - -
339E PRO* 3.3 6.6 - - - +
340E THR* 2.9 28.1 + - - +
341E ARG 3.3 0.2 - - - -
342E ALA* 1.3 76.9 - - + +
344E GLY* 1.3 59.8 + - - +
346E ASP* 3.9 0.4 - - - +
347E VAL* 3.1 32.7 + - - +
340F THR* 4.9 5.6 + - - +
342F ALA* 3.8 17.3 - - + -
343F GLU* 4.7 6.7 - - + +
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Residues in contact with GLY 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E LEU* 4.8 1.3 - - - +
339E PRO* 5.5 3.1 - - - -
340E THR 3.2 12.5 + - - -
341E ARG* 3.4 3.8 + - - -
342E ALA 3.3 0.6 - - - -
343E GLU* 1.3 77.1 - - - +
345E SER* 1.3 63.0 + - - +
347E VAL 3.8 0.2 + - - -
348E ALA* 3.5 19.8 + - - +
380E ILE* 3.9 25.2 - - - +
302F ALA 5.6 6.5 - - - -
303F GLU* 6.5 0.2 - - - -
306F PHE* 5.0 3.3 - - - -
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Residues in contact with SER 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E ARG 3.2 10.1 + - - -
342E ALA 3.4 1.7 + - - -
344E GLY* 1.3 73.7 - - - +
346E ASP* 1.3 60.9 + - - +
348E ALA* 3.4 6.6 + - - +
349E ASN* 2.8 42.9 + - - +
293F ARG* 4.0 7.6 - - - -
306F PHE* 4.5 13.8 - - - +
309F GLN* 4.2 11.9 - - - -
346F ASP* 2.5 38.0 + - - +
349F ASN* 6.2 0.2 - - - -
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Residues in contact with ASP 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293E ARG* 2.7 38.6 + - - -
309E GLN* 4.5 3.1 + - - +
329E MET* 3.7 15.6 - - - +
342E ALA 3.2 16.6 + - - +
343E GLU 3.9 2.0 - - - +
344E GLY 3.3 0.2 - - - -
345E SER* 1.3 79.1 + - - +
347E VAL* 1.3 60.3 + - - +
349E ASN* 3.3 7.4 + - - +
350E ALA* 2.9 27.6 + - - +
342F ALA* 3.4 17.5 - - + +
345F SER* 2.6 30.5 + - - +
346F ASP* 5.5 1.1 - - - +
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Residues in contact with VAL 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329E MET* 3.6 46.0 - - + +
330E LEU* 3.9 13.0 - - + -
343E GLU 3.1 19.0 + - - +
344E GLY 4.1 1.6 - - - +
345E SER 3.4 0.2 - - - -
346E ASP* 1.3 74.9 - - - +
348E ALA* 1.3 59.8 + - - +
350E ALA* 3.4 8.8 + - - +
351E VAL* 3.0 24.2 + - + +
358E ILE* 4.0 20.1 - - + +
377E GLN* 4.3 11.2 - - + +
380E ILE* 3.8 26.9 - - + -
381E ALA 5.2 0.2 - - - +
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Residues in contact with ALA 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E GLY 3.5 9.6 + - - +
345E SER 3.4 8.0 + - - +
346E ASP 3.2 0.4 - - - -
347E VAL* 1.3 76.5 - - - +
349E ASN* 1.3 53.7 + - - +
351E VAL* 3.1 5.5 + - - +
352E LEU* 2.8 39.7 + - + +
380E ILE* 3.6 11.3 - - + +
384E ALA* 3.7 8.8 - - + +
306F PHE* 3.6 44.9 - - + -
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Residues in contact with ASN 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E GLN* 5.2 2.0 - - - +
345E SER* 2.8 34.6 + - - +
346E ASP* 3.6 8.3 + - - +
348E ALA* 1.3 72.4 - - - +
350E ALA* 1.3 55.5 + - - +
352E LEU* 4.1 8.2 - - - +
353E ASP* 2.8 45.1 + - - +
309F GLN* 5.8 1.2 + - - -
310F LYS* 3.7 29.5 - - - +
345F SER* 4.9 0.7 - - - +
346F ASP* 5.5 0.2 - - - -
349F ASN* 3.1 50.6 - - - +
353F ASP* 5.5 0.5 - - - +
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Residues in contact with ALA 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E GLN* 4.3 6.7 - - - +
313E ILE* 4.3 0.2 - - - +
325E CYS* 3.9 32.8 - - + -
329E MET* 4.7 1.6 - - + -
346E ASP 2.9 14.2 + - - +
347E VAL* 3.4 13.7 - - - +
348E ALA 3.2 0.2 - - - -
349E ASN* 1.3 76.8 - - - +
351E VAL* 1.3 58.1 + - - +
353E ASP* 3.6 9.7 - - - +
354E GLY 3.4 4.5 + - - -
355E ALA* 3.2 28.2 + - - +
358E ILE* 4.2 12.1 - - + -
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Residues in contact with VAL 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E THR* 3.9 15.3 - - + +
347E VAL* 3.0 21.8 - - + +
348E ALA* 3.6 5.2 - - - +
350E ALA* 1.3 72.8 - - + +
352E LEU* 1.3 65.4 + - - +
353E ASP 3.2 0.4 - - - -
354E GLY 3.2 1.9 + - - -
355E ALA 4.4 1.1 - - - +
358E ILE* 5.0 4.9 - - + +
381E ALA* 4.0 16.4 - - + +
384E ALA* 3.7 25.4 - - + +
385E GLU* 3.9 16.8 - - + +
388E MET* 3.4 4.6 - - - +
466E ARG* 2.4 56.3 + - - +
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Residues in contact with LEU 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348E ALA 2.8 30.8 + - - +
349E ASN* 3.8 11.7 - - - +
351E VAL* 1.3 71.7 - - - +
353E ASP* 1.3 63.6 + - - +
354E GLY 3.5 0.2 + - - -
384E ALA* 3.5 24.7 - - + +
387E ALA* 3.8 25.8 - - + +
388E MET* 3.6 21.1 - - + +
393E LEU* 6.1 0.5 - - - +
306F PHE* 4.0 16.8 - - + -
310F LYS* 3.7 32.5 - - + +
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Residues in contact with ASP 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E GLN* 3.3 23.7 + - - -
310E LYS* 2.9 41.8 + - - +
313E ILE* 3.5 19.9 - - + +
317E ASN* 3.6 4.7 + - - -
349E ASN* 2.8 27.7 + - - +
350E ALA 3.6 6.7 - - - +
352E LEU* 1.3 78.4 - - - +
354E GLY* 1.3 56.0 + - - +
388E MET* 4.8 0.7 - - - +
393E LEU* 5.6 4.7 - - - +
26F LEU* 5.9 0.9 - - - +
29F MET* 3.5 30.6 - - + +
349F ASN* 4.8 0.7 + - - -
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Residues in contact with GLY 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E ILE* 3.8 1.1 - - - -
317E ASN* 3.1 21.8 - - - +
350E ALA 3.4 0.4 + - - -
351E VAL 3.2 5.6 + - - -
353E ASP* 1.3 79.5 - - - +
355E ALA* 1.3 69.1 + - - +
356E ASP 3.4 1.2 + - - -
388E MET* 4.2 7.6 - - - -
393E LEU* 6.2 0.9 - - - -
444E ARG* 3.1 24.0 + - - -
466E ARG* 3.3 16.6 + - - -
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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
------------------------------------------------------------
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