Contacts of the helix formed by residues 304 - 320 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C ILE* 3.2 40.0 + - + +
35C ASP* 5.2 1.0 - - - +
36C SER 4.8 0.8 + - - -
37C PRO* 4.7 7.7 - - - +
38C PRO* 4.5 8.1 - - - +
383C GLU* 2.9 35.8 + - + +
300D ILE* 4.0 11.2 - - + -
301D PRO* 2.9 41.7 + - + +
303D GLU* 1.3 85.5 - - + +
305D VAL* 1.3 64.0 + - - +
306D PHE 3.4 1.8 - - - -
307D LEU* 3.3 27.2 + - + +
308D ALA 3.4 4.5 + - - -
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Residues in contact with VAL 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C ARG* 4.9 7.6 - - + -
293D ARG* 3.6 36.6 - - + +
296D LEU* 4.3 14.8 - - + -
297D GLY* 3.5 30.3 - - - +
300D ILE* 4.1 12.1 - - + -
301D PRO 4.0 3.6 - - - +
302D ALA* 3.2 24.0 + - - +
304D LYS* 1.3 75.4 - - - +
306D PHE* 1.3 60.3 + - - +
308D ALA* 3.2 4.9 + - - +
309D GLN* 2.9 26.5 + - - +
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Residues in contact with PHE 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 5.3 0.7 - - + -
344C GLY 5.3 1.6 - - - +
345C SER* 4.5 15.3 - - - -
348C ALA* 3.5 31.0 - - + -
352C LEU* 4.1 17.5 - - + -
380C ILE* 4.6 4.0 - - + -
383C GLU* 3.5 30.3 - - + -
384C ALA* 3.6 15.3 - - + -
387C ALA* 4.3 5.6 - - + -
302D ALA 4.9 0.8 + - - -
303D GLU 3.6 23.3 - - - -
305D VAL* 1.3 77.2 - - - +
307D LEU* 1.3 84.1 + - + +
309D GLN* 3.3 12.2 + - - +
310D LYS* 3.0 55.9 + - + +
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Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLN* 3.4 26.0 - - - +
32C LEU* 3.9 25.0 - - + +
33C ASP 4.0 7.2 - - - +
34C ILE* 4.1 10.1 - - + +
383C GLU* 3.4 32.3 - - - +
387C ALA* 3.8 15.3 - - + -
304D LYS* 3.3 22.2 + - + +
306D PHE* 1.3 109.3 - - + +
308D ALA* 1.3 60.7 + - - +
310D LYS* 3.4 2.1 + - - +
311D MET* 3.0 30.7 + - - +
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Residues in contact with ALA 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ILE* 3.8 20.1 - - + +
276D VAL* 4.2 12.1 - - + -
296D LEU* 4.0 13.5 - - + -
300D ILE* 4.8 2.0 - - + -
304D LYS 3.4 3.0 + - - +
305D VAL* 3.2 9.7 + - - +
307D LEU* 1.3 79.1 - - - +
309D GLN* 1.3 63.5 + - - +
311D MET* 3.9 8.2 - - - +
312D MET* 3.0 48.2 + - + +
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Residues in contact with GLN 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C SER* 4.5 9.0 - - - -
291D VAL* 4.0 25.0 - - + +
293D ARG* 2.7 32.0 + - - +
305D VAL* 2.9 13.9 + - - +
306D PHE* 3.4 13.3 - - - +
308D ALA* 1.3 77.6 - - - +
310D LYS* 1.3 58.6 + - - +
312D MET* 3.9 1.8 - - - +
313D ILE* 3.0 46.2 + - + +
325D CYS* 3.4 25.7 - - - -
346D ASP* 4.9 2.8 + - - -
349D ASN* 5.9 1.0 - - - +
350D ALA* 4.0 13.1 - - - +
353D ASP* 3.6 19.8 + - - +
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Residues in contact with LYS 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C MET* 3.5 30.5 - - + +
32C LEU* 3.9 21.8 - - + -
349C ASN* 3.2 35.3 + - - +
352C LEU* 3.7 21.0 - - + +
306D PHE* 3.0 34.3 + - + +
309D GLN* 1.3 75.2 - - + +
311D MET* 1.3 60.7 + - - +
313D ILE* 4.6 2.9 - - - -
314D GLY* 3.0 25.5 + - - -
349D ASN* 5.0 0.6 - - - +
353D ASP* 2.7 47.6 + - - +
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Residues in contact with MET 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET 3.2 14.5 + - - +
30C CYS* 3.6 19.4 - - - +
32C LEU* 3.3 23.8 - - + +
33C ASP* 6.2 0.2 - - - -
34C ILE* 5.9 1.3 - - + +
276D VAL* 3.6 38.8 - - + +
279D PHE* 4.2 9.0 - - + -
307D LEU 3.0 17.9 + - - +
308D ALA* 3.9 7.0 - - - +
310D LYS* 1.3 77.5 - - - +
312D MET* 1.3 78.9 + - + +
314D GLY* 4.1 0.5 - - - -
315D ARG* 3.3 54.2 + - - +
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Residues in contact with MET 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ILE* 3.7 35.4 - - + -
276D VAL* 4.3 8.7 - - + -
279D PHE* 3.5 31.0 - - + -
289D ILE* 4.2 4.3 - - + -
291D VAL* 3.8 36.3 - - + -
296D LEU* 3.9 11.0 - - + -
308D ALA* 3.0 47.3 + - + +
309D GLN 3.9 2.2 - - - +
311D MET* 1.3 85.0 - - + +
313D ILE* 1.3 64.3 + - - +
315D ARG 3.3 1.6 + - - -
316D CYS* 3.0 29.8 + - - -
323D VAL* 4.5 0.4 - - - -
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Residues in contact with ILE 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET* 4.9 0.2 - - + -
291D VAL* 4.7 4.3 - - + -
309D GLN* 3.0 46.1 + - + +
310D LYS 4.0 3.1 - - - +
312D MET* 1.3 74.7 - - - +
314D GLY* 1.3 56.9 + - - +
316D CYS* 3.2 3.3 + - - +
317D ASN* 2.8 40.4 + - - +
323D VAL* 3.9 25.4 - - + -
325D CYS* 5.0 4.0 - - + +
350D ALA 4.4 0.2 - - - +
353D ASP* 3.4 48.9 - - + +
354D GLY 3.5 15.5 - - - +
355D ALA* 3.6 14.4 - - + +
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Residues in contact with GLY 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 3.5 20.1 - - - +
29C MET* 4.4 9.6 - - - +
30C CYS* 3.7 10.8 - - - -
310D LYS 3.0 16.9 + - - -
311D MET 4.1 1.1 - - - -
312D MET 3.4 0.2 - - - -
313D ILE* 1.3 76.5 - - - +
315D ARG* 1.3 51.2 + - - +
317D ASN* 3.3 8.4 + - - +
318D ARG* 2.8 33.1 + - - +
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Residues in contact with ARG 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C CYS* 2.8 32.1 + - + -
31C ARG* 4.7 4.4 - - - +
32C LEU 5.4 0.4 + - - -
276D VAL 5.9 0.4 + - - -
279D PHE* 3.6 35.7 - - + +
280D ASP* 2.7 43.1 + - - +
283D LEU* 4.1 7.3 - - + +
311D MET* 3.3 32.8 + - - +
313D ILE 3.3 0.2 - - - -
314D GLY* 1.3 72.1 - - - +
316D CYS* 1.3 56.1 + - - +
318D ARG* 3.1 34.3 + - - +
319D ALA* 2.7 36.7 + - - +
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Residues in contact with CYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D PHE* 4.0 3.6 - - - -
283D LEU* 3.7 24.7 - - - -
289D ILE* 3.7 19.3 - - - -
312D MET 3.0 19.2 + - - +
313D ILE 3.6 1.8 - - - +
315D ARG* 1.3 72.7 - - - +
317D ASN* 1.3 61.3 + - - +
319D ALA* 4.4 5.2 - - - +
320D GLY* 2.9 24.4 + - - -
321D LYS 3.1 27.2 + - - +
322D PRO 4.0 4.0 - - - -
323D VAL* 3.5 30.1 - - + -
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Residues in contact with ASN 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 4.4 7.4 - - + +
313D ILE* 2.8 21.6 + - - +
314D GLY* 3.4 10.8 - - - +
316D CYS* 1.3 77.8 - - - +
318D ARG* 1.3 61.0 + - - +
320D GLY* 3.7 7.8 + - - -
323D VAL* 4.5 0.5 - - - +
353D ASP 3.2 25.5 + - - -
354D GLY* 2.8 29.4 - - - +
356D ASP* 4.2 3.6 - - - +
393D LEU* 5.5 6.4 - - + +
397D LEU* 3.4 27.6 - - + +
442D ARG* 4.4 10.0 + - - +
444D ARG* 3.1 21.1 + - + +
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Residues in contact with ARG 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 4.4 12.8 - - + +
27C GLU* 2.8 39.7 + - - -
30C CYS* 3.4 22.6 - - - +
280D ASP* 5.3 1.6 + - - -
314D GLY 2.8 20.0 + - - +
315D ARG* 3.1 40.6 + - - +
317D ASN* 1.3 74.4 - - - +
319D ALA* 1.3 56.6 + - - +
397D LEU* 4.6 2.2 - - - +
400D ALA* 3.6 34.4 - - + +
401D SER* 5.1 2.8 - - - -
442D ARG* 2.8 19.1 + - - -
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Residues in contact with ALA 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D LEU* 3.8 21.8 - - + -
315D ARG 2.7 20.0 + - - +
316D CYS* 4.2 2.7 - - - +
318D ARG* 1.3 75.0 - - - +
320D GLY* 1.3 60.0 + - - +
321D LYS* 3.6 17.9 - - + +
442D ARG* 3.0 17.4 + - - +
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Residues in contact with GLY 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D CYS 2.9 7.6 + - - -
317D ASN* 3.7 2.6 + - - -
318D ARG 3.5 1.6 - - - -
319D ALA* 1.3 78.6 - - - +
321D LYS* 1.3 63.6 + - - +
438D HIS* 4.9 1.6 - - - +
439D GLN* 5.6 1.2 - - - +
442D ARG* 3.5 35.7 - - - +
465D TYR* 3.4 22.3 + - - -
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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