Contacts of the helix formed by residues 304 - 320 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A ILE* 3.8 13.1 - - + +
301A PRO* 2.8 42.3 + - + +
303A GLU* 1.3 83.3 - - + +
305A VAL* 1.3 64.5 + - - +
306A PHE 3.4 2.5 - - - -
307A LEU* 3.2 23.8 + - + +
308A ALA 3.3 9.7 + - - -
34B ILE* 3.1 39.1 + - + +
35B ASP* 5.1 0.8 - - - +
36B SER 4.5 5.5 + - - -
37B PRO* 4.6 4.4 - - - +
38B PRO* 4.5 8.4 - - - +
383B GLU* 2.7 35.6 + - + +
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 3.5 37.0 - - + +
296A LEU* 4.1 14.8 - - + +
297A GLY* 3.4 34.8 - - - +
300A ILE* 4.3 7.2 - - + -
301A PRO 4.2 2.9 - - - +
302A ALA* 3.2 21.8 + - - +
304A LYS* 1.3 78.2 - - - +
306A PHE* 1.3 58.1 + - - +
308A ALA* 3.1 4.8 + - - +
309A GLN* 2.9 28.4 + - + +
341B ARG* 4.6 9.6 - - + +
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Residues in contact with PHE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ALA 4.8 0.6 + - - -
303A GLU* 3.0 29.4 - - - -
305A VAL* 1.3 78.7 - - - +
307A LEU* 1.3 84.5 + - + +
309A GLN* 3.7 11.2 + - - +
310A LYS* 3.3 38.7 + - + +
32B LEU* 5.8 0.7 - - + -
344B GLY 5.5 0.9 - - - -
345B SER* 4.3 19.0 - - - -
348B ALA* 3.5 30.1 - - + -
349B ASN* 5.5 0.9 - - - +
352B LEU* 4.4 13.9 - - + -
380B ILE* 4.2 8.3 - - + -
383B GLU* 3.5 15.3 - - + -
384B ALA* 3.4 37.0 - - + -
387B ALA* 4.1 8.3 - - + -
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A LYS* 3.2 25.7 + - + +
305A VAL 3.1 0.2 - - - -
306A PHE* 1.3 95.4 - - + +
308A ALA* 1.3 65.2 + - - +
310A LYS* 3.3 2.6 + - - +
311A MET* 3.1 26.1 + - - +
16B GLN* 3.5 28.0 - - - +
32B LEU* 3.8 34.7 - - + +
33B ASP 4.6 2.5 - - - +
34B ILE* 3.8 13.9 - - + +
383B GLU* 3.3 32.3 - - - +
387B ALA* 4.0 14.1 - - + -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A VAL* 4.6 10.8 - - + -
296A LEU* 4.0 13.5 - - + -
300A ILE* 4.5 6.1 - - + -
304A LYS 3.3 4.3 + - - +
305A VAL 3.1 8.2 + - - +
307A LEU* 1.3 79.3 - - - +
309A GLN* 1.3 62.1 + - - +
311A MET* 3.9 9.2 - - - +
312A MET* 3.1 46.9 + - + +
32B LEU 5.7 0.2 - - - -
34B ILE* 3.7 19.0 - - + +
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Residues in contact with GLN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A VAL* 4.0 28.2 - - + +
293A ARG* 3.1 29.4 + - - +
305A VAL* 2.9 17.4 + - + +
306A PHE* 3.8 10.1 - - - +
308A ALA* 1.3 76.3 - - - +
310A LYS* 1.3 59.2 + - - +
312A MET* 3.2 3.7 + - - +
313A ILE* 2.8 52.0 + - + +
325A CYS* 4.0 18.5 - - - -
346A ASP* 4.7 2.9 + - - +
349A ASN* 5.2 0.4 - - - +
350A ALA* 4.2 8.9 - - - +
353A ASP* 3.4 23.0 + - - -
345B SER* 4.8 7.7 - - - -
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Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A PHE* 3.3 25.7 + - + +
307A LEU 3.3 4.3 + - - +
309A GLN* 1.3 76.1 - - + +
311A MET* 1.3 61.0 + - - +
313A ILE* 4.5 2.9 - - - +
314A GLY* 2.9 25.6 + - - -
353A ASP* 2.7 43.6 + - - +
25B PHE* 6.1 3.4 - - - -
29B MET* 3.3 32.9 - - + +
32B LEU* 4.0 21.3 - - + -
349B ASN* 3.4 30.4 - - - +
352B LEU* 3.8 20.7 - - + +
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Residues in contact with MET 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A VAL* 3.8 34.3 - - + +
279A PHE* 4.0 12.1 - - + -
307A LEU 3.1 13.9 + - - +
308A ALA* 3.9 7.2 - - - +
310A LYS* 1.3 78.7 - - - +
312A MET* 1.3 79.4 + - + +
314A GLY* 3.9 0.5 - - - -
315A ARG* 3.1 76.1 + - - +
29B MET 3.3 14.6 + - - +
30B CYS* 3.6 7.2 - - - +
32B LEU* 3.4 27.1 - - + +
34B ILE* 6.2 0.2 - - + -
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ILE* 3.7 42.0 - - + -
276A VAL* 4.6 3.1 - - + -
279A PHE* 3.6 26.7 - - + -
289A ILE* 4.3 3.4 - - + -
291A VAL* 3.8 36.1 - - + -
296A LEU* 4.0 10.1 - - + -
308A ALA* 3.1 46.4 + - + +
309A GLN 3.6 3.1 - - - +
311A MET* 1.3 88.8 - - + +
313A ILE* 1.3 64.5 + - - +
316A CYS* 3.0 31.0 + - - -
323A VAL* 4.3 0.9 - - - -
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Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A VAL* 4.8 2.7 - - + -
309A GLN* 2.8 55.1 + - + +
310A LYS* 4.1 4.0 - - - +
312A MET* 1.3 70.8 - - - +
314A GLY* 1.3 63.1 + - - +
316A CYS* 3.4 1.9 + - - +
317A ASN* 3.0 30.4 + - - +
323A VAL* 3.8 25.1 - - + -
325A CYS* 5.0 5.6 - - + -
350A ALA 4.3 6.7 - - - +
353A ASP* 3.3 41.5 - - + +
354A GLY 3.5 22.2 - - - +
355A ALA* 4.3 7.6 - - + -
29B MET* 4.6 0.7 - - + -
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Residues in contact with GLY 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LYS 2.9 19.4 + - - -
311A MET 3.9 1.1 - - - -
313A ILE* 1.3 77.4 - - - +
315A ARG* 1.3 55.9 + - - +
317A ASN* 3.3 4.8 + - - +
318A ARG* 3.0 23.6 + - - +
26B LEU* 3.3 26.0 - - - +
29B MET* 4.3 10.1 - - - +
30B CYS* 3.4 11.2 - - - -
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Residues in contact with ARG 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 3.7 23.5 - - + +
280A ASP* 2.6 48.3 + - - +
283A LEU* 3.9 6.6 - - + +
311A MET* 3.1 42.1 + - - +
314A GLY* 1.3 72.4 - - - +
316A CYS* 1.3 61.3 + - - +
318A ARG* 3.3 32.1 + - - +
319A ALA* 2.9 29.1 + - - +
30B CYS* 3.0 35.4 + - + -
31B ARG* 5.0 2.2 - - - +
32B LEU 5.0 2.0 + - - -
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Residues in contact with CYS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A PHE* 3.7 9.0 - - - -
283A LEU* 3.8 13.0 - - + -
289A ILE* 3.6 38.4 - - - -
312A MET 3.0 25.6 + - - +
313A ILE 3.8 0.9 - - - +
315A ARG* 1.3 73.7 - - - +
317A ASN* 1.3 59.1 + - - +
319A ALA* 3.4 1.2 + - - +
320A GLY 2.8 23.4 + - - -
321A LYS 2.9 30.0 + - - +
322A PRO 4.7 0.7 - - - -
323A VAL* 3.7 20.2 - - + -
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Residues in contact with ASN 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ILE* 3.0 19.9 + - - +
314A GLY* 3.4 10.4 - - - +
316A CYS* 1.3 76.6 - - - +
318A ARG* 1.3 62.5 + - - +
320A GLY* 3.2 13.4 + - - -
321A LYS 5.0 0.2 - - - -
323A VAL* 4.3 4.7 - - - +
353A ASP 3.5 19.2 + - - -
354A GLY* 2.9 31.5 + - - +
356A ASP* 4.3 3.6 - - - +
393A LEU* 5.5 9.3 - - - +
397A LEU* 3.7 25.2 - - + +
442A ARG* 4.4 7.8 + - - +
444A ARG* 3.9 19.5 + - + +
26B LEU* 4.6 6.6 - - + +
29B MET* 6.1 0.2 - - - -
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ASP* 5.4 1.2 + - - -
314A GLY 3.0 12.4 + - - +
315A ARG* 3.3 43.0 + - - +
316A CYS 3.3 0.2 - - - -
317A ASN* 1.3 76.2 - - - +
319A ALA* 1.3 52.6 + - - +
397A LEU* 4.5 8.1 - - - +
400A ALA* 3.8 35.0 - - + +
401A SER* 5.0 2.1 - - - -
442A ARG* 2.6 31.5 + - - -
26B LEU* 4.6 7.2 - - + +
27B GLU* 3.1 35.2 + - - -
30B CYS* 3.8 19.9 + - - +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 4.3 18.4 - - + -
315A ARG 2.9 16.1 + - - +
316A CYS* 4.1 3.4 - - - +
318A ARG* 1.3 75.4 - - - +
320A GLY* 1.3 62.8 + - - +
321A LYS* 3.4 19.3 + - + +
442A ARG* 4.0 12.9 + - - +
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A CYS 2.8 7.7 + - - -
317A ASN* 3.2 9.1 + - - -
318A ARG 3.2 4.9 + - - -
319A ALA* 1.3 78.7 - - - +
321A LYS* 1.3 61.0 + - - +
438A HIS* 5.3 2.3 - - - +
442A ARG* 3.9 32.0 - - - +
444A ARG* 6.3 0.7 - - - -
465A TYR* 4.0 16.8 + - - -
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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
------------------------------------------------------------
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