Contacts of the helix formed by residues 304 - 320 (chain F) 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 LYS 304 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ILE* 3.1 46.7 + - + +
35E ASP 5.3 0.4 - - - -
36E SER 4.0 11.5 + - - -
37E PRO* 4.6 4.4 - - - +
38E PRO* 4.4 6.1 - - - +
383E GLU* 2.8 35.6 + - - +
300F ILE* 3.9 12.8 - - + +
301F PRO* 3.1 35.8 + - + +
303F GLU* 1.3 79.9 - - + +
305F VAL* 1.3 62.2 + - - +
306F PHE* 3.4 1.1 - - - -
307F LEU* 3.3 28.8 + - + +
308F ALA 3.4 0.9 + - - -
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Residues in contact with VAL 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E ARG* 4.9 9.0 - - + +
293F ARG* 3.8 35.2 - - + +
296F LEU* 4.4 9.1 - - + +
297F GLY* 3.6 32.5 - - - +
300F ILE* 4.3 11.4 - - + -
301F PRO 3.7 8.3 - - - +
302F ALA* 3.2 18.6 - - + +
303F GLU 3.0 1.8 + - - -
304F LYS* 1.3 75.6 - - - +
306F PHE* 1.3 62.5 + - - +
308F ALA* 3.0 6.6 + - - +
309F GLN* 2.9 27.8 + - + +
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Residues in contact with PHE 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E GLY 5.0 3.6 - - - +
345E SER* 4.5 18.4 - - - +
348E ALA* 3.6 26.9 - - + -
352E LEU* 4.0 15.9 - - + -
380E ILE* 4.3 6.3 - - + -
383E GLU* 3.7 19.1 - - + -
384E ALA* 3.3 41.3 - - + -
387E ALA* 4.0 3.8 - - + -
302F ALA 4.7 0.2 + - - -
303F GLU 2.8 29.6 - - - -
305F VAL* 1.3 80.2 - - - +
307F LEU* 1.3 79.3 + - + +
309F GLN* 3.7 13.0 - - - +
310F LYS* 3.1 45.4 + - + +
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Residues in contact with LEU 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN* 3.5 24.0 - - - +
32E LEU* 3.9 31.4 - - + +
33E ASP 4.0 6.5 - - - +
34E ILE* 3.8 14.8 - - + +
383E GLU* 3.6 26.0 - - - +
387E ALA* 3.8 28.0 - - + -
304F LYS* 3.3 20.8 + - + +
305F VAL 3.1 0.2 - - - -
306F PHE* 1.3 99.2 - - + +
308F ALA* 1.3 57.6 + - - +
310F LYS* 4.2 2.1 - - - -
311F MET* 3.0 29.5 + - - +
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Residues in contact with ALA 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ILE* 3.9 12.3 - - + +
276F VAL* 4.3 15.5 - - + -
296F LEU* 4.4 11.4 - - + -
300F ILE* 4.7 1.1 - - + -
304F LYS 3.4 7.2 + - - +
305F VAL* 3.0 11.0 + - - +
307F LEU* 1.3 77.3 - - - +
309F GLN* 1.3 59.4 + - - +
311F MET* 3.3 8.7 + - - +
312F MET* 2.9 53.5 + - + +
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Residues in contact with GLN 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345E SER* 4.2 12.6 - - - -
349E ASN* 5.8 1.2 + - - -
291F VAL* 4.0 26.8 - - + +
293F ARG* 3.1 30.9 + - - +
305F VAL* 2.9 17.5 + - + +
306F PHE* 3.7 10.1 - - - +
308F ALA* 1.3 76.6 - - - +
310F LYS* 1.3 61.9 + - - +
312F MET* 3.2 2.8 + - - +
313F ILE* 2.9 46.0 + - + +
325F CYS* 4.7 7.6 - - - -
346F ASP* 5.4 1.4 + - - -
349F ASN* 5.0 1.6 - - - +
350F ALA* 4.4 10.9 - - - +
353F ASP* 2.8 28.3 + - - -
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Residues in contact with LYS 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E PHE* 5.8 5.9 - - - -
29E MET* 3.3 37.4 - - + +
32E LEU* 4.3 20.6 - - + -
349E ASN* 3.7 19.8 - - - +
352E LEU* 3.7 30.2 - - + +
306F PHE* 3.1 28.6 + - + +
307F LEU 4.2 2.2 - - - +
309F GLN* 1.3 79.9 - - - +
311F MET* 1.3 64.2 + - - +
313F ILE* 4.7 2.2 - - - -
314F GLY 3.1 19.4 + - - -
349F ASN* 5.4 0.2 - - - +
353F ASP* 2.8 38.2 + - - +
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Residues in contact with MET 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E MET 3.7 11.8 + - - +
30E CYS* 3.6 15.9 - - - +
32E LEU 3.4 22.7 - - - +
276F VAL* 3.8 37.7 - - + +
279F PHE* 4.3 9.9 - - + -
307F LEU 3.0 20.6 + - - +
308F ALA* 3.5 7.0 - - - +
310F LYS* 1.3 76.2 - - - +
312F MET* 1.3 79.8 + - + +
314F GLY* 4.2 0.5 - - - -
315F ARG* 3.2 62.7 + - - +
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Residues in contact with MET 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F ILE* 3.6 39.9 - - + -
276F VAL* 4.5 3.4 - - + -
279F PHE* 3.4 28.9 - - + -
289F ILE* 4.3 2.9 - - + -
291F VAL* 3.8 36.8 - - + -
296F LEU* 3.8 11.9 - - + -
308F ALA* 2.9 45.6 + - + +
309F GLN 3.7 2.5 - - - +
311F MET* 1.3 85.4 - - + +
313F ILE* 1.3 65.8 + - - +
315F ARG* 3.9 0.7 - - - +
316F CYS* 3.0 31.5 + - - -
323F VAL* 4.5 1.1 - - + -
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Residues in contact with ILE 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E MET* 4.3 1.8 - - + -
291F VAL* 4.9 2.7 - - + -
309F GLN* 2.9 42.5 + - + +
310F LYS 4.2 2.5 - - - +
312F MET* 1.3 75.1 - - - +
314F GLY* 1.3 59.0 + - - +
316F CYS* 3.2 1.4 + - - +
317F ASN* 2.8 52.5 + - - +
323F VAL* 3.9 27.4 - - + -
325F CYS* 5.2 6.7 - - + -
350F ALA* 4.2 9.4 - - - +
353F ASP* 3.5 37.9 - - + +
354F GLY 3.6 11.0 - - - +
355F ALA* 4.4 10.3 - - + +
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Residues in contact with GLY 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LEU* 3.8 17.6 - - - +
29E MET* 4.2 8.9 - - - +
30E CYS* 3.4 16.1 - - - -
310F LYS 3.1 17.4 + - - -
313F ILE* 1.3 79.5 - - - +
315F ARG* 1.3 55.2 + - - +
317F ASN* 3.3 3.9 + - - +
318F ARG* 2.9 29.5 + - - +
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Residues in contact with ARG 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E CYS* 3.0 37.5 + - + +
31E ARG* 4.9 3.8 + - - +
276F VAL 5.3 1.4 + - - -
277F ARG 6.0 0.2 + - - -
279F PHE* 3.8 27.4 - - + +
280F ASP* 2.8 38.8 + - - +
283F LEU* 3.9 8.5 - - + +
311F MET* 3.2 42.0 + - - +
312F MET 4.0 0.2 - - - +
313F ILE 3.3 0.4 - - - -
314F GLY* 1.3 74.8 - - - +
316F CYS* 1.3 57.7 + - - +
318F ARG* 3.5 33.0 + - - +
319F ALA* 3.1 27.2 + - - +
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Residues in contact with CYS 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F PHE* 3.8 13.0 - - - -
283F LEU* 3.6 26.0 - - - -
289F ILE* 3.8 16.4 - - - -
312F MET 3.0 24.6 + - - +
313F ILE 3.7 3.4 - - - +
315F ARG* 1.3 74.4 - - - +
317F ASN* 1.3 55.1 + - - +
319F ALA* 3.1 5.8 + - - +
320F GLY 2.7 31.0 + - - -
321F LYS 3.1 26.8 + - - +
322F PRO 4.7 2.0 - - - -
323F VAL* 3.7 18.4 - - + -
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Residues in contact with ASN 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU* 4.3 8.4 - - + +
313F ILE* 2.8 30.4 + - - +
314F GLY* 3.5 7.6 - - - +
316F CYS* 1.3 71.5 - - - +
318F ARG* 1.3 62.4 + - - +
320F GLY* 3.5 11.1 + - - +
321F LYS 5.1 0.4 - - - -
323F VAL* 4.0 2.9 - - - +
353F ASP 3.6 5.1 + - - -
354F GLY* 3.0 34.7 + - - +
356F ASP* 3.8 3.8 - - - +
393F LEU* 5.5 6.0 - - + +
397F LEU* 3.4 25.3 - - + +
442F ARG* 4.3 11.2 + - - +
444F ARG* 2.9 32.6 + - + +
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Residues in contact with ARG 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU* 4.4 7.6 - - + +
27E GLU* 3.3 35.4 + - - -
30E CYS* 3.7 23.0 - - - +
280F ASP* 5.0 4.0 + - - -
283F LEU* 6.0 1.2 - - - +
314F GLY 2.9 16.0 + - - +
315F ARG* 3.5 35.0 + - - +
317F ASN* 1.3 75.6 - - - +
319F ALA* 1.3 55.2 + - - +
397F LEU* 4.3 10.1 - - - +
400F ALA* 3.7 29.9 - - + +
401F SER* 5.1 3.3 - - - -
442F ARG* 2.7 25.1 + - - -
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Residues in contact with ALA 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283F LEU* 4.2 20.2 - - + -
315F ARG 3.1 15.6 + - - +
316F CYS* 3.1 6.1 + - - +
318F ARG* 1.3 77.7 - - - +
320F GLY* 1.3 61.8 + - - +
321F LYS* 3.7 16.4 + - + +
442F ARG* 3.8 12.6 + - - +
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Residues in contact with GLY 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316F CYS 2.7 8.6 + - - -
317F ASN* 3.5 5.4 + - - -
318F ARG 3.4 3.0 - - - -
319F ALA* 1.3 79.8 - - - +
321F LYS* 1.3 59.3 + - - +
438F HIS* 5.3 3.1 - - - +
439F GLN* 5.8 0.3 - - - +
442F ARG* 3.7 36.5 - - - +
465F TYR* 4.2 14.6 - - - -
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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
------------------------------------------------------------
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