Contacts of the helix formed by residues 304 - 320 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ILE* 2.8 40.6 + - + +
35G ASP* 5.1 0.2 - - - +
36G SER 4.6 4.9 + - - -
37G PRO* 4.8 4.0 - - - +
38G PRO* 4.6 8.2 - - - +
383G GLU* 3.0 35.1 + - - +
300H ILE* 3.8 12.4 - - + +
301H PRO* 3.0 43.7 + - + +
303H GLU* 1.3 78.7 - - + +
305H VAL* 1.3 63.2 + - - +
306H PHE 3.3 2.7 - - - -
307H LEU* 3.1 31.5 + - + +
308H ALA 3.5 4.0 + - - -
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Residues in contact with VAL 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341G ARG* 4.5 13.2 - - + +
344G GLY* 6.5 1.1 - - - -
291H VAL* 5.6 0.8 - - + +
293H ARG* 3.8 36.6 - - + +
296H LEU* 4.7 7.4 - - + +
297H GLY* 3.7 30.5 - - - +
300H ILE* 4.2 10.5 - - + -
301H PRO 4.0 2.9 - - - +
302H ALA* 3.1 25.4 + - + +
303H GLU 3.4 0.4 - - - -
304H LYS* 1.3 77.7 - - - +
306H PHE* 1.3 64.3 + - - +
307H LEU 3.2 0.3 + - - -
308H ALA* 3.3 5.5 + - - +
309H GLN* 3.0 21.6 + - + +
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Residues in contact with PHE 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344G GLY 4.9 3.3 - - - +
345G SER* 4.4 15.5 - - - -
348G ALA* 3.6 27.6 - - + -
349G ASN* 5.8 0.4 - - - +
352G LEU* 3.7 28.7 - - + -
380G ILE* 4.7 2.9 - - + -
383G GLU* 3.9 10.8 - - + -
384G ALA* 3.5 26.7 - - + -
387G ALA* 3.9 11.2 - - + -
302H ALA 4.9 0.4 + - - -
303H GLU 3.2 28.5 - - - -
305H VAL* 1.3 79.3 - - - +
307H LEU* 1.3 81.8 + - + +
309H GLN* 3.6 16.0 - - - +
310H LYS* 3.0 48.0 + - + +
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Residues in contact with LEU 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G GLN* 3.4 32.3 - - - +
32G LEU* 3.8 23.1 - - + +
33G ASP 4.3 4.5 - - - +
34G ILE* 3.8 13.9 - - + +
383G GLU* 3.8 18.6 - - - +
387G ALA* 3.7 27.8 - - + -
304H LYS* 3.1 25.1 + - + +
306H PHE* 1.3 94.4 - - + +
308H ALA* 1.3 59.3 + - - +
310H LYS* 3.3 4.2 + - - +
311H MET* 2.8 32.8 + - - +
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Residues in contact with ALA 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ILE* 3.6 18.7 - - + +
276H VAL* 3.9 16.2 - - + -
296H LEU* 4.5 8.3 - - + -
300H ILE* 4.8 5.8 - - + -
304H LYS 3.5 3.1 + - - +
305H VAL* 3.3 8.8 + - - +
307H LEU* 1.3 77.3 - - - +
309H GLN* 1.3 58.1 + - - +
311H MET* 3.6 8.2 - - - +
312H MET* 2.9 54.3 + - + +
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Residues in contact with GLN 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345G SER* 4.3 9.7 - - - -
349G ASN* 5.7 0.3 - - - +
291H VAL* 3.9 27.0 - - + +
293H ARG* 3.6 21.6 + - + +
305H VAL* 3.0 17.0 + - + +
306H PHE* 3.6 16.9 - - - +
307H LEU 3.3 0.2 - - - -
308H ALA* 1.3 76.4 - - - +
310H LYS* 1.3 60.2 + - - +
312H MET* 4.0 2.1 - - - +
313H ILE* 3.0 47.7 + - + +
325H CYS* 3.3 30.3 - - - +
346H ASP* 4.9 2.0 + - - -
350H ALA* 4.0 16.4 - - - +
353H ASP* 4.3 11.2 + - - +
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Residues in contact with LYS 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G PHE* 6.4 1.5 - - + -
29G MET* 3.2 33.6 - - + +
32G LEU* 3.8 23.3 - - + -
349G ASN* 3.2 33.5 + - - +
352G LEU* 4.0 18.2 - - + -
306H PHE* 3.0 36.4 + - + +
309H GLN* 1.3 77.9 - - - +
311H MET* 1.3 59.0 + - - +
313H ILE* 4.6 1.1 - - - -
314H GLY* 3.0 24.8 + - - -
349H ASN* 5.2 0.2 - - - +
353H ASP* 2.7 44.7 + - - +
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Residues in contact with MET 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G MET 3.3 12.3 + - - +
30G CYS* 3.6 16.7 - - - +
32G LEU* 3.3 24.7 - - + +
34G ILE* 6.0 0.7 - - + -
276H VAL* 3.7 39.0 - - + +
279H PHE* 4.0 10.5 - - + -
307H LEU 2.8 18.6 + - - +
308H ALA* 3.6 6.7 - - - +
310H LYS* 1.3 76.9 - - - +
312H MET* 1.3 72.4 + - + +
314H GLY* 3.9 0.7 - - - -
315H ARG* 3.1 58.3 + - - +
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Residues in contact with MET 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H ILE* 3.7 35.4 - - + -
276H VAL* 4.3 6.3 - - + -
279H PHE* 3.5 32.4 - - + -
289H ILE* 4.6 4.0 - - + -
291H VAL* 3.8 34.8 - - + -
296H LEU* 4.1 13.5 - - + -
308H ALA* 2.9 48.1 + - + +
309H GLN 4.1 2.0 - - - +
311H MET* 1.3 81.9 - - + +
313H ILE* 1.3 65.7 + - - +
316H CYS* 3.1 30.6 + - - +
323H VAL* 4.4 1.6 - - - -
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Residues in contact with ILE 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G MET* 4.3 2.2 - - + -
291H VAL* 4.8 3.1 - - + -
309H GLN* 3.0 41.7 + - + +
310H LYS 4.1 2.7 - - - +
312H MET* 1.3 74.7 - - - +
314H GLY* 1.3 67.2 + - - +
316H CYS* 3.2 2.6 + - - +
317H ASN* 2.9 41.9 + - - +
323H VAL* 3.8 26.5 - - + -
325H CYS* 5.0 5.2 - - + -
350H ALA 4.2 2.0 - - - +
353H ASP* 3.7 24.5 - - + +
354H GLY 3.7 21.1 - - - +
355H ALA* 3.9 19.5 - - + -
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Residues in contact with GLY 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LEU* 3.8 14.8 - - - +
29G MET* 4.2 12.8 - - - +
30G CYS* 3.3 15.5 - - - -
310H LYS 3.0 18.1 + - - -
311H MET 3.9 0.7 - - - -
313H ILE* 1.3 78.3 - - - +
315H ARG* 1.3 56.1 + - - +
317H ASN* 3.3 4.5 + - - +
318H ARG* 3.0 27.7 + - - +
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Residues in contact with ARG 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G CYS* 3.1 38.0 + - + +
31G ARG* 5.4 1.4 - - - +
32G LEU 5.5 0.8 + - - -
276H VAL 5.4 1.4 + - - -
277H ARG 5.8 1.4 + - - -
279H PHE* 3.6 37.1 - - + +
280H ASP* 2.8 43.5 + - - +
283H LEU* 3.8 7.1 - - + +
311H MET* 3.1 35.0 + - - +
314H GLY* 1.3 74.7 - - - +
316H CYS* 1.3 57.3 + - - +
318H ARG* 3.5 26.4 + - - +
319H ALA* 3.1 27.5 + - - +
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Residues in contact with CYS 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279H PHE* 4.1 4.0 - - - -
283H LEU* 3.7 22.7 - - - -
289H ILE* 3.6 31.6 - - - -
312H MET 3.1 24.9 + - - +
313H ILE 3.6 3.1 - - - +
315H ARG* 1.3 75.4 - - - +
317H ASN* 1.3 61.0 + - - +
319H ALA* 3.2 1.7 + - - +
320H GLY* 2.8 25.8 + - - -
321H LYS 3.2 23.7 + - - +
322H PRO 4.4 2.0 - - - -
323H VAL* 3.6 19.3 - - + -
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Residues in contact with ASN 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LEU* 4.4 8.0 - - + +
313H ILE* 2.9 27.2 + - - +
314H GLY* 3.7 6.5 - - - +
316H CYS* 1.3 72.5 - - - +
318H ARG* 1.3 66.5 + - - +
319H ALA 3.3 0.7 + - - -
320H GLY* 3.4 11.3 + - - -
321H LYS 5.3 0.2 - - - -
323H VAL* 4.4 1.6 - - - +
353H ASP 3.7 4.9 + - - -
354H GLY* 2.9 43.1 + - - +
356H ASP* 4.0 5.4 - - - +
393H LEU* 5.6 4.6 - - + +
397H LEU* 3.4 25.6 - - + +
442H ARG* 4.4 10.5 + - - +
444H ARG* 3.1 24.6 + - - +
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Residues in contact with ARG 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LEU* 4.5 6.5 - - + +
27G GLU* 3.4 26.4 + - - +
30G CYS* 3.5 27.9 - - - +
280H ASP* 4.4 8.9 + - - -
283H LEU* 6.3 0.2 - - - +
314H GLY 3.0 16.7 + - - +
315H ARG* 3.5 30.4 + - - +
317H ASN* 1.3 75.8 - - - +
319H ALA* 1.3 56.2 + - - +
397H LEU* 4.2 9.9 - - - +
400H ALA* 3.6 35.6 - - + +
401H SER* 5.3 0.7 - - - -
442H ARG* 2.9 20.6 + - - -
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Residues in contact with ALA 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H LEU* 3.9 22.0 - - + -
315H ARG 3.1 17.4 + - - +
316H CYS* 3.2 4.9 + - - +
317H ASN 3.2 0.2 - - - -
318H ARG* 1.3 79.5 - - - +
320H GLY* 1.3 59.0 + - - +
321H LYS* 3.5 13.3 - - + +
442H ARG* 3.2 19.7 + - - +
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Residues in contact with GLY 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H CYS 2.8 7.2 + - - -
317H ASN* 3.4 5.9 + - - -
319H ALA* 1.3 76.9 - - - +
321H LYS* 1.3 63.3 + - - +
438H HIS* 5.1 2.3 - - - +
442H ARG* 3.8 34.8 - - - +
465H TYR* 4.0 19.1 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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