Contacts of the helix formed by residues 304 - 320 (chain B) in PDB entry 3SRH
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ILE* 4.0 11.7 - - + +
301B PRO* 2.9 41.7 + - + +
303B GLU* 1.3 85.8 - - + +
305B VAL* 1.3 62.8 + - - +
306B PHE 3.4 1.8 - - - -
307B LEU* 3.2 35.9 + - + +
308B ALA 3.4 4.7 + - - -
34C ILE* 3.2 41.7 + - + +
36C SER 4.3 6.7 + - - -
37C PRO* 4.5 4.2 - - - +
38C PRO* 4.3 22.2 - - - +
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ARG* 3.9 41.5 - - + +
296B LEU* 4.6 7.4 - - + -
297B GLY* 3.8 31.9 - - - +
300B ILE* 4.4 11.9 - - + -
301B PRO 4.1 3.4 - - - +
302B ALA* 3.5 21.8 - - + +
303B GLU 3.3 1.8 - - - -
304B LYS* 1.3 75.7 - - - +
306B PHE* 1.3 63.6 + - - +
307B LEU 3.1 0.5 + - - -
308B ALA* 3.1 5.0 + - - +
309B GLN* 2.9 26.1 + - + +
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA 5.1 0.6 + - - -
303B GLU 3.2 28.0 - - - -
305B VAL* 1.3 78.6 - - - +
307B LEU* 1.3 92.5 + - + +
309B GLN* 3.6 14.4 - - - +
310B LYS* 3.0 58.6 + - + +
32C LEU* 5.4 0.9 - - + -
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LYS* 3.2 29.3 + - + +
305B VAL 3.1 0.8 - - - -
306B PHE* 1.3 111.1 - - + +
308B ALA* 1.3 60.2 + - - +
310B LYS* 3.4 2.1 + - - +
311B MET* 2.9 31.5 + - - +
16C GLN* 3.9 25.4 - - + +
32C LEU* 4.0 39.3 - - + +
33C ASP 4.0 8.7 - - - +
34C ILE* 4.0 14.8 - - + +
36C SER 5.5 0.7 - - - +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B VAL* 4.3 11.7 - - + -
296B LEU* 4.0 16.4 - - + -
300B ILE* 4.6 2.5 - - + -
304B LYS 3.4 3.4 + - - +
305B VAL 3.1 7.2 + - - +
307B LEU* 1.3 79.0 - - - +
309B GLN* 1.3 57.4 + - - +
311B MET* 3.6 9.1 - - + +
312B MET* 2.9 53.8 + - + +
34C ILE* 4.0 17.7 - - + +
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Residues in contact with GLN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL* 3.8 27.2 - - + +
293B ARG* 3.3 33.0 + - - +
305B VAL* 2.9 17.6 + - + +
306B PHE* 3.6 13.2 - - - +
308B ALA* 1.3 77.1 - - - +
310B LYS* 1.3 61.4 + - - +
312B MET* 4.0 1.6 - - - +
313B ILE* 3.1 44.6 + - + +
325B CYS* 4.0 17.8 - - - -
346B ASP* 4.7 2.7 + - - +
349B ASN* 5.2 1.2 - - - +
350B ALA* 4.3 9.9 - - - +
353B ASP* 3.0 25.5 + - - -
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Residues in contact with LYS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PHE* 3.0 46.8 + - + +
309B GLN* 1.3 76.3 - - - +
311B MET* 1.3 60.9 + - - +
313B ILE* 4.6 2.2 - - - +
314B GLY* 3.0 25.8 + - - -
349B ASN* 5.5 7.6 - - - +
353B ASP* 2.7 45.6 + - - +
25C PHE* 6.1 2.6 - - - -
29C MET* 3.4 28.6 - - + +
32C LEU* 3.9 21.1 - - + -
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Residues in contact with MET 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B VAL* 3.6 44.0 - - + +
279B PHE* 4.3 4.7 - - + -
307B LEU 2.9 18.6 + - - +
308B ALA* 3.6 7.2 - - - +
310B LYS* 1.3 77.0 - - - +
312B MET* 1.3 81.3 + - + +
314B GLY* 3.9 0.9 - - - -
315B ARG* 3.2 58.1 + - - +
29C MET 3.1 13.6 + - - +
30C CYS* 3.8 18.2 - - - +
32C LEU 3.4 24.0 - - - +
34C ILE* 6.3 0.2 - - + -
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Residues in contact with MET 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 3.7 34.5 - - + -
276B VAL* 4.7 1.6 - - + -
279B PHE* 3.5 38.3 - - + -
289B ILE* 4.3 9.4 - - + -
291B VAL* 3.7 31.9 - - + -
296B LEU* 4.2 5.8 - - + -
308B ALA* 2.9 45.2 + - + +
309B GLN 4.0 2.7 - - - +
311B MET* 1.3 86.3 - - + +
313B ILE* 1.3 66.1 + - - +
315B ARG* 3.3 2.6 + - - +
316B CYS* 2.9 30.1 + - - -
323B VAL* 4.7 0.7 - - - -
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Residues in contact with ILE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL* 4.7 3.6 - - + -
309B GLN* 3.1 38.7 + - + +
310B LYS 4.1 2.2 - - - +
312B MET* 1.3 75.6 - - - +
314B GLY* 1.3 63.9 + - - +
316B CYS* 3.2 1.6 + - - +
317B ASN* 2.9 24.7 + - - +
323B VAL* 3.9 26.0 - - + -
325B CYS* 5.2 4.9 - - + +
350B ALA* 4.2 2.5 - - - +
353B ASP* 3.4 48.5 - - + +
354B GLY* 3.4 22.7 - - - +
355B ALA* 3.8 19.1 - - + -
29C MET* 4.5 0.2 - - + -
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Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LYS 3.0 18.3 + - - -
311B MET 3.9 0.4 - - - -
313B ILE* 1.3 78.3 - - - +
315B ARG* 1.3 56.2 + - - +
317B ASN* 3.3 3.8 + - - +
318B ARG* 3.0 27.5 + - - +
26C LEU* 3.9 11.8 - - - +
29C MET* 3.9 15.4 - - - +
30C CYS* 3.4 16.9 - - - -
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Residues in contact with ARG 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B VAL 4.7 3.8 + - - -
277B ARG 5.7 1.2 + - - -
279B PHE* 3.7 39.9 - - + +
280B ASP* 2.7 43.4 + - - -
283B LEU* 3.7 7.4 - - + +
311B MET* 3.2 32.1 + - - +
312B MET 3.3 0.4 + - - +
314B GLY* 1.3 75.5 - - - +
316B CYS* 1.3 58.1 + - - +
318B ARG* 3.5 27.2 + - - +
319B ALA* 3.0 29.6 + - - +
30C CYS* 3.1 37.0 + - + +
31C ARG* 5.1 2.4 - - - +
32C LEU 5.5 0.8 + - - -
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Residues in contact with CYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PHE* 4.0 5.2 - - - -
283B LEU* 3.8 15.9 - - - -
289B ILE* 3.7 37.7 - - - -
312B MET 2.9 22.9 + - - +
313B ILE 3.2 4.5 + - - +
315B ARG* 1.3 75.9 - - - +
317B ASN* 1.3 55.8 + - - +
319B ALA* 4.6 0.9 - - - -
320B GLY* 2.8 27.0 + - - -
321B LYS 2.9 30.4 + - - +
322B PRO 4.3 0.7 - - - -
323B VAL* 3.8 20.4 - - + -
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Residues in contact with ASN 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B ILE* 2.9 15.2 + - - +
314B GLY 3.3 8.3 + - - +
316B CYS* 1.3 75.7 - - - +
318B ARG* 1.3 62.3 + - - +
320B GLY* 3.3 12.4 + - - +
323B VAL* 4.8 1.9 - - - +
353B ASP 3.6 8.7 + - - -
354B GLY* 3.0 30.4 - - - +
356B ASP* 4.5 1.7 - - - +
393B LEU* 5.1 9.5 - - - +
397B LEU* 3.9 20.3 - - + +
442B ARG* 4.4 11.0 + - - +
444B ARG* 2.9 33.7 + - + +
26C LEU* 4.1 17.3 - - + +
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Residues in contact with ARG 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ASP* 4.7 5.7 + - - -
314B GLY 3.0 15.8 + - - +
315B ARG* 3.7 33.6 + - - +
316B CYS 3.3 0.2 - - - -
317B ASN* 1.3 78.4 - - - +
319B ALA* 1.3 56.3 + - - +
397B LEU* 5.0 1.8 - - - -
400B LEU* 3.8 33.9 - - + +
442B ARG* 3.4 19.6 + - - +
26C LEU* 4.4 12.5 - - + +
27C GLU* 3.1 33.1 + - - -
30C CYS* 4.1 17.0 - - - +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B LEU* 3.8 22.9 - - + -
315B ARG 3.0 18.2 + - - +
316B CYS 4.2 2.2 - - - +
318B ARG* 1.3 77.7 - - - +
320B GLY* 1.3 62.3 + - - +
321B LYS* 3.5 18.3 - - + +
442B ARG* 4.3 10.4 + - - -
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Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B CYS 2.8 10.1 + - - -
317B ASN* 3.3 12.9 + - - -
319B ALA* 1.3 80.7 - - - +
321B LYS* 1.3 58.6 + - - +
438B HIS 5.5 0.7 - - - +
442B ARG* 4.1 30.3 - - - +
465B TYR* 3.8 19.9 + - - -
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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