Contacts of the helix formed by residues 304 - 320 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300G ILE* 3.8 13.0 - - + -
301G PRO* 2.9 42.8 + - + +
303G GLU* 1.3 81.9 - - + +
305G VAL* 1.3 66.5 + - - +
306G PHE 3.2 2.7 - - - -
307G LEU* 2.9 30.7 + - + +
308G ALA 3.4 3.5 + - - -
34H ILE* 3.1 39.8 + - + +
35H ASP 5.5 0.2 - - - -
36H SER 4.4 7.3 + - - -
37H PRO* 4.8 3.2 - - - +
38H PRO* 4.4 5.1 - - - +
383H GLU* 2.7 34.6 + - - +
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Residues in contact with VAL 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G VAL* 5.7 0.2 - - + -
293G ARG* 3.7 37.2 - - + +
296G LEU* 4.4 11.9 - - + +
297G GLY* 3.6 29.8 - - - +
300G ILE* 4.0 13.9 - - + +
301G PRO 3.9 7.9 - - - +
302G ALA* 3.4 19.1 - - - +
303G GLU 3.5 1.2 - - - -
304G LYS* 1.3 77.4 - - - +
306G PHE* 1.3 58.7 + - - +
308G ALA* 3.0 4.7 + - - +
309G GLN* 2.8 29.4 + - + +
341H ARG* 4.9 7.2 - - - -
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Residues in contact with PHE 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G ALA 5.0 0.6 + - - -
303G GLU 3.2 29.4 - - - -
304G LYS 3.2 0.6 - - - -
305G VAL* 1.3 77.9 - - - +
307G LEU* 1.3 90.3 + - + +
309G GLN* 3.7 10.7 - - - +
310G LYS* 3.1 43.2 + - + +
32H LEU* 5.7 0.4 - - + -
344H GLY 5.3 1.1 - - - +
345H SER* 4.5 17.9 - - - -
348H ALA* 3.5 29.4 - - + -
349H ASN* 5.7 0.4 - - - +
352H LEU* 3.8 28.3 - - + -
380H ILE* 4.7 1.8 - - + -
383H GLU* 3.8 10.3 - - + -
384H ALA* 3.5 27.4 - - + -
387H ALA* 3.8 10.1 - - + -
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Residues in contact with LEU 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304G LYS* 2.9 23.1 + - + +
306G PHE* 1.3 94.2 - - + +
308G ALA* 1.3 61.0 + - - +
310G LYS* 3.4 4.1 + - - +
311G MET* 2.9 32.4 + - - +
16H GLN* 3.5 31.2 - - - +
32H LEU* 4.0 23.3 - - + +
33H ASP 4.2 6.3 - - - +
34H ILE* 4.1 12.1 - - + +
383H GLU* 3.7 26.9 - - - +
387H ALA* 3.7 28.7 - - + -
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Residues in contact with ALA 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G VAL* 4.6 8.5 - - + -
296G LEU* 4.2 13.5 - - + -
300G ILE* 4.5 4.3 - - + -
304G LYS 3.4 1.4 + - - +
305G VAL* 3.0 12.9 + - - +
307G LEU* 1.3 79.0 - - - +
309G GLN* 1.3 63.7 + - - +
311G MET* 3.3 10.1 + - - +
312G MET* 2.9 45.8 + - + +
34H ILE* 3.9 19.2 - - + +
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Residues in contact with GLN 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G VAL* 3.9 26.1 - - + +
293G ARG* 2.8 33.8 + - - +
305G VAL* 2.8 19.7 + - + +
306G PHE* 3.7 9.3 - - - +
308G ALA* 1.3 73.1 - - - +
310G LYS* 1.3 58.2 + - - +
312G MET* 3.2 3.1 + - - +
313G ILE* 2.9 54.0 + - + +
325G CYS* 3.6 22.7 - - - -
346G ASP* 5.4 1.0 + - - -
349G ASN* 6.1 0.4 - - - +
350G ALA* 4.0 11.7 - - - +
353G ASP* 3.8 14.1 + - - -
345H SER* 4.8 7.4 - - - -
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Residues in contact with LYS 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G PHE* 3.1 33.7 + - + +
307G LEU 4.0 2.2 - - - +
309G GLN* 1.3 78.1 - - + +
311G MET* 1.3 65.3 + - - +
313G ILE* 4.6 3.6 - - - -
314G GLY* 3.0 18.9 + - - -
349G ASN* 5.4 0.6 - - - +
353G ASP* 2.7 47.6 + - - +
25H PHE* 5.9 3.0 - - - -
29H MET* 3.4 26.9 - - + +
32H LEU* 4.1 19.5 - - + -
349H ASN* 3.2 32.7 - - - +
352H LEU* 3.7 20.2 - - + +
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Residues in contact with MET 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G VAL* 3.7 39.0 - - + +
279G PHE* 4.3 7.2 - - + -
307G LEU 2.9 18.8 + - - +
308G ALA* 3.5 4.3 - - - +
310G LYS* 1.3 76.1 - - - +
312G MET* 1.3 78.5 + - + +
314G GLY* 3.3 2.6 + - - -
315G ARG* 3.1 52.4 + - - +
29H MET 3.3 13.2 + - - +
30H CYS* 3.4 22.6 - - - +
32H LEU 3.5 19.1 - - - +
34H ILE* 6.3 0.4 - - + -
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Residues in contact with MET 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ILE* 3.8 36.8 - - + -
276G VAL* 4.4 4.9 - - + -
279G PHE* 3.6 30.2 - - + -
289G ILE* 4.5 3.1 - - + -
291G VAL* 3.9 28.3 - - + -
296G LEU* 3.9 18.8 - - + -
308G ALA* 2.9 47.5 + - + +
309G GLN 3.7 2.9 - - - +
311G MET* 1.3 84.9 - - + +
313G ILE* 1.3 64.0 + - - +
316G CYS* 3.1 32.2 + - - -
323G VAL* 4.7 0.9 - - - -
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Residues in contact with ILE 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G VAL* 4.7 3.1 - - + -
309G GLN* 2.9 47.0 + - + +
310G LYS 4.1 3.4 - - - +
312G MET* 1.3 72.9 - - - +
314G GLY* 1.3 66.8 + - - +
316G CYS* 3.3 1.0 + - - +
317G ASN* 2.9 31.6 + - - +
323G VAL* 4.2 24.0 - - + -
325G CYS* 5.0 3.1 - - + -
350G ALA 4.1 7.9 - - - +
353G ASP* 3.3 46.7 - - + +
354G GLY* 3.5 21.5 - - - +
355G ALA* 4.3 9.0 - - + +
29H MET* 4.6 0.2 - - + -
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Residues in contact with GLY 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G LYS 3.0 16.1 + - - -
311G MET 3.3 3.3 + - - -
313G ILE* 1.3 78.2 - - - +
315G ARG* 1.3 56.3 + - - +
317G ASN* 3.3 3.9 + - - +
318G ARG* 2.9 27.4 + - - +
26H LEU* 4.0 12.0 - - - +
29H MET* 4.0 13.2 - - - +
30H CYS* 3.3 18.0 - - - -
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Residues in contact with ARG 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G VAL 5.6 1.0 + - - -
279G PHE* 3.7 26.4 - - + +
280G ASP* 2.7 46.1 + - - +
283G LEU* 3.7 7.3 - - + +
311G MET* 3.1 35.6 + - - +
314G GLY* 1.3 72.8 - - - +
316G CYS* 1.3 59.7 - - - +
318G ARG* 3.5 30.3 + - - +
319G ALA* 2.9 30.1 + - - +
30H CYS* 3.1 35.9 + - + -
31H ARG* 5.0 2.4 - - - +
32H LEU 5.6 0.4 + - - -
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Residues in contact with CYS 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279G PHE* 3.7 9.9 - - - -
283G LEU* 3.7 28.7 - - - -
289G ILE* 3.8 12.1 - - - -
312G MET 3.1 26.0 + - - +
313G ILE 3.6 4.0 - - - +
314G GLY 3.3 0.4 - - - -
315G ARG* 1.3 76.4 - - - +
317G ASN* 1.3 55.4 + - - +
319G ALA* 3.7 0.4 - - - -
320G GLY* 2.8 28.2 + - - -
321G LYS 3.0 29.2 + - - +
322G PRO 4.5 1.3 - - - -
323G VAL* 3.7 26.7 - - + -
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Residues in contact with ASN 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G ILE* 2.9 20.4 + - - +
314G GLY* 3.6 5.3 - - - +
316G CYS* 1.3 73.4 - - - +
318G ARG* 1.3 67.3 + - - +
320G GLY* 3.2 13.6 + - - -
323G VAL* 4.1 5.7 - - - +
353G ASP 3.9 5.9 + - - -
354G GLY* 3.2 26.9 + - - +
356G ASP* 4.1 1.4 - - - +
393G LEU* 5.1 11.9 - - - +
397G LEU* 3.4 25.6 - - + +
442G ARG* 4.5 8.0 + - - +
444G ARG* 3.1 36.9 + - - +
26H LEU* 4.4 7.3 - - + +
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Residues in contact with ARG 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G ASP* 5.3 2.2 + - - -
314G GLY 2.9 16.4 + - - +
315G ARG* 3.5 34.8 + - - +
317G ASN* 1.3 76.6 - - - +
319G ALA* 1.3 52.4 + - - +
397G LEU* 4.1 9.2 - - - +
400G ALA* 3.7 35.6 - - + +
401G SER* 4.6 5.4 - - - -
442G ARG* 2.8 28.8 + - - -
26H LEU* 4.6 6.3 - - + +
27H GLU* 3.1 33.2 + - - +
30H CYS* 3.5 28.3 - - - +
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Residues in contact with ALA 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283G LEU* 4.0 20.2 - - + -
315G ARG 2.9 17.9 + - - +
316G CYS* 4.2 2.5 - - - +
318G ARG* 1.3 76.8 - - - +
320G GLY* 1.3 58.7 + - - +
321G LYS* 3.4 14.0 + - + +
442G ARG* 3.6 15.7 + - - +
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Residues in contact with GLY 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G CYS 2.8 7.5 + - - -
317G ASN* 3.2 12.0 + - - -
319G ALA* 1.3 78.9 - - - +
321G LYS* 1.3 63.0 + - - +
438G HIS 4.9 0.9 - - - +
442G ARG* 3.8 33.1 - - - +
465G TYR* 3.9 18.2 - - - -
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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
------------------------------------------------------------
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