Contacts of the helix formed by residues 304 - 320 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C ILE* 3.8 11.2 - - + -
301C PRO* 3.0 41.3 + - + +
303C GLU* 1.3 81.3 - - + +
305C VAL* 1.3 54.6 + - - +
306C PHE 3.2 2.7 - - - -
307C LEU* 2.7 41.7 + - + +
308C ALA 3.2 4.0 + - - -
34D ILE* 3.0 45.9 + - + +
36D SER 4.3 10.1 + - - -
37D PRO* 4.8 3.4 - - - +
38D PRO* 4.6 3.6 - - - +
383D GLU* 3.1 37.3 + - - +
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Residues in contact with VAL 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ARG* 3.7 35.2 - - + +
296C LEU* 4.3 15.0 - - + +
297C GLY* 3.6 32.1 - - - +
300C ILE* 4.5 5.6 - - + -
301C PRO 4.0 2.9 - - - +
302C ALA* 3.2 21.6 + - + +
304C LYS* 1.3 76.0 - - - +
306C PHE* 1.3 57.8 + - - +
308C ALA* 3.1 8.9 + - - +
309C GLN* 2.8 30.4 + - + +
341D ARG* 5.0 7.9 - - + -
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Residues in contact with PHE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ALA 4.7 1.2 + - - -
303C GLU 3.2 27.8 - - - -
304C LYS 3.1 0.8 + - - -
305C VAL* 1.3 76.9 - - - +
307C LEU* 1.3 79.4 + - + +
309C GLN* 3.7 9.0 - - - +
310C LYS* 3.0 56.9 + - + +
32D LEU* 5.7 0.2 - - + -
344D GLY 5.1 1.8 - - - +
345D SER* 4.6 17.0 - - - -
348D ALA* 3.5 28.9 - - + -
349D ASN* 6.3 0.4 - - - +
352D LEU* 3.9 11.4 - - + -
380D ILE* 4.6 3.6 - - + -
383D GLU* 3.6 16.6 - - + -
384D ALA* 3.3 30.7 - - + -
387D ALA* 3.9 15.9 - - + -
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C LYS* 2.7 26.2 + - + +
306C PHE* 1.3 90.2 - - + +
308C ALA* 1.3 64.7 + - - +
310C LYS* 3.3 4.8 + - - +
311C MET* 3.0 25.7 + - - +
16D GLN* 3.5 28.0 - - - +
32D LEU* 4.0 23.5 - - + +
34D ILE* 3.7 23.3 - - + +
383D GLU* 3.3 26.7 - - - +
387D ALA* 3.6 27.8 - - + -
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Residues in contact with ALA 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL* 4.6 15.3 - - + -
296C LEU* 4.4 11.9 - - + -
300C ILE* 4.6 4.7 - - + -
304C LYS 3.2 2.1 + - - +
305C VAL* 3.1 11.3 + - - +
307C LEU* 1.3 78.8 - - - +
309C GLN* 1.3 61.7 + - - +
311C MET* 3.7 9.2 - - - +
312C MET* 3.1 43.4 + - + +
32D LEU 5.7 0.4 - - - -
34D ILE* 3.7 17.9 - - + +
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Residues in contact with GLN 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C VAL* 3.8 28.4 - - + +
293C ARG* 2.9 36.2 + - - +
305C VAL* 2.8 21.7 + - + +
306C PHE* 3.7 7.8 - - - +
308C ALA* 1.3 72.5 - - - +
310C LYS* 1.3 59.4 + - - +
312C MET* 3.3 3.1 + - - +
313C ILE* 2.9 49.3 + - + +
325C CYS* 3.7 12.3 - - - -
346C ASP* 5.6 1.8 + - - -
350C ALA* 4.4 7.1 - - - +
353C ASP* 3.1 26.7 + - - -
345D SER* 5.1 5.2 - - - -
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Residues in contact with LYS 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C PHE* 3.0 36.3 + - + +
307C LEU 3.9 2.7 - - - +
309C GLN* 1.3 79.1 - - - +
311C MET* 1.3 53.3 + - - +
313C ILE* 4.7 1.8 - - - -
314C GLY* 2.8 30.0 + - - -
349C ASN* 5.2 0.8 - - - +
353C ASP* 2.7 40.5 + - - +
29D MET* 3.3 30.7 - - + +
32D LEU* 4.1 22.0 - - + -
349D ASN* 3.3 23.8 - - - +
352D LEU* 3.7 27.1 - - + +
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Residues in contact with MET 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C VAL* 3.8 36.6 - - + +
279C PHE* 3.9 11.9 - - + -
307C LEU 3.0 17.4 + - - +
308C ALA* 3.7 6.3 - - - +
310C LYS* 1.3 76.5 - - - +
312C MET* 1.3 74.8 + - + +
314C GLY* 3.2 1.4 + - - -
315C ARG* 2.8 74.1 + - - +
29D MET 3.3 14.2 + - - +
30D CYS* 3.8 9.8 - - - +
32D LEU 3.5 22.2 - - - +
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Residues in contact with MET 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C ILE* 3.7 39.0 - - + -
276C VAL* 4.9 2.9 - - + -
279C PHE* 3.5 31.1 - - + -
289C ILE* 4.5 4.7 - - + -
291C VAL* 3.8 36.6 - - + -
296C LEU* 3.9 16.8 - - + -
308C ALA* 3.1 32.9 + - + +
309C GLN 3.8 2.7 - - - +
311C MET* 1.3 85.3 - - + +
313C ILE* 1.3 66.3 + - - +
315C ARG* 3.2 1.4 + - - -
316C CYS* 2.9 31.3 + - - -
323C VAL* 4.7 0.2 - - - -
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Residues in contact with ILE 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C VAL* 4.4 3.6 - - + -
309C GLN* 2.9 49.8 + - + +
310C LYS 4.0 2.5 - - - +
312C MET* 1.3 73.7 - - - +
314C GLY* 1.3 62.6 + - - +
316C CYS* 3.9 0.5 - - - +
317C ASN* 2.9 31.0 + - - +
323C VAL* 3.7 26.9 - - + -
325C CYS* 4.9 6.3 - - + -
350C ALA 4.3 0.7 - - - +
353C ASP* 3.3 38.6 - - + +
354C GLY 3.6 20.4 - - - +
355C ALA* 3.9 20.4 - - + +
29D MET* 4.9 0.2 - - + -
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Residues in contact with GLY 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C LYS 2.8 20.1 + - - -
311C MET 3.4 1.3 - - - -
312C MET 3.1 0.4 - - - -
313C ILE* 1.3 79.7 - - - +
315C ARG* 1.3 60.2 + - - +
317C ASN* 3.4 5.6 + - - +
318C ARG* 3.3 14.9 + - - +
353C ASP 5.5 0.2 - - - -
26D LEU* 3.7 14.8 - - - +
29D MET* 4.5 10.8 - - - -
30D CYS* 3.4 19.8 - - - -
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Residues in contact with ARG 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276C VAL 5.7 0.6 + - - -
279C PHE* 3.6 24.3 - - + +
280C ASP* 2.8 42.4 + - - +
283C LEU* 4.0 8.0 - - + +
311C MET* 2.8 46.5 + - - +
314C GLY* 1.3 69.3 - - - +
316C CYS* 1.3 65.5 + - - +
318C ARG* 3.3 24.7 + - - +
319C ALA* 3.1 21.1 + - - +
30D CYS* 3.0 43.7 + - + +
31D ARG* 5.0 2.6 - - - +
32D LEU 5.5 0.4 + - - -
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Residues in contact with CYS 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279C PHE* 3.8 8.3 - - - -
283C LEU* 3.7 29.8 - - - -
289C ILE* 3.8 24.9 - - - -
312C MET 2.9 22.7 + - - +
313C ILE 3.9 1.8 - - - +
315C ARG* 1.3 74.0 - - - +
317C ASN* 1.3 53.9 + - - +
319C ALA* 3.0 2.7 + - - -
320C GLY 2.8 31.2 + - - -
321C LYS 3.2 27.3 + - - +
322C PRO 5.0 0.2 - - - -
323C VAL* 3.8 19.3 - - + -
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Residues in contact with ASN 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ILE* 2.9 21.5 + - - +
314C GLY* 3.6 5.6 - - - +
316C CYS* 1.3 75.7 - - - +
318C ARG* 1.3 62.1 + - - +
319C ALA 3.3 0.7 + - - -
320C GLY* 3.3 12.2 + - - +
323C VAL* 4.1 5.5 - - - +
353C ASP 3.8 6.9 + - - -
354C GLY* 3.0 26.9 + - - +
356C ASP* 4.4 1.4 - - - +
393C LEU* 5.1 8.3 - - - +
397C LEU* 3.6 24.9 - - + +
442C ARG* 4.4 11.2 + - - +
444C ARG* 3.1 37.5 + - - +
26D LEU* 4.6 9.7 - - + +
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Residues in contact with ARG 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ASP* 5.5 3.8 + - - -
314C GLY 3.3 8.1 + - - +
315C ARG* 3.3 33.0 + - - +
317C ASN* 1.3 78.3 - - - +
319C ALA* 1.3 53.7 + - - +
397C LEU* 4.3 8.0 - - - +
400C ALA* 3.5 35.8 - - + +
401C SER* 5.1 3.8 - - - -
442C ARG* 2.7 23.3 + - - -
26D LEU* 4.7 8.7 - - + +
27D GLU* 3.5 24.5 + - - +
30D CYS* 3.4 34.9 - - - +
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Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C LEU* 4.0 20.2 - - + -
315C ARG 3.1 11.1 + - - +
316C CYS 3.0 8.3 + - - +
318C ARG* 1.3 77.2 - - - +
320C GLY* 1.3 58.9 + - - +
321C LYS* 4.2 19.2 - - + +
442C ARG* 3.0 18.6 + - - +
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Residues in contact with GLY 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C CYS 2.8 6.3 + - - -
317C ASN* 3.3 6.0 + - - -
319C ALA* 1.3 77.7 - - - +
321C LYS* 1.3 62.7 + - - +
438C HIS* 5.2 2.6 - - - +
442C ARG* 3.7 32.3 - - - +
465C TYR* 3.8 20.3 - - - -
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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
------------------------------------------------------------
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