Contacts of the helix formed by residues 280 - 295 (chain K) in PDB entry 5G04
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 280 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251K TYR* 3.7 35.9 - - + +
275K LEU* 3.1 14.8 + - + +
278K LEU* 3.6 43.9 + - + +
279K ASN* 1.3 71.0 - - - +
281K ALA* 1.3 65.4 - - - +
282K ASN 3.2 2.9 - - - -
283K GLU* 3.0 39.0 + - + +
284K LEU* 3.1 11.6 + - - +
311K MET* 4.1 3.2 - - - +
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Residues in contact with ALA 281 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557F LYS* 5.2 1.3 - - - +
279K ASN 3.0 9.8 + - - +
280K LYS* 1.3 72.2 - - - +
282K ASN* 1.3 59.7 + - - +
284K LEU* 3.2 2.8 + - - +
285K PHE* 2.8 31.8 + - - +
308K TYR* 3.7 14.8 - - + -
311K MET* 3.6 24.2 - - + -
312K VAL* 4.9 11.2 - - + +
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Residues in contact with ASN 282 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554F VAL* 3.9 15.2 - - + +
557F LYS* 3.0 38.9 + - - +
558F ASP* 3.7 38.8 + - - +
561F ASP* 4.8 10.6 + - - +
280K LYS 3.2 0.4 - - - -
281K ALA* 1.3 78.1 - - - +
283K GLU* 1.3 75.7 + - - +
285K PHE* 3.3 2.1 + - - +
286K TYR* 3.0 23.0 + - - +
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Residues in contact with GLU 283 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K TYR* 4.3 9.2 - - - +
271K HIS* 5.6 2.4 - - + -
275K LEU* 3.8 15.9 - - + +
280K LYS* 3.0 48.6 + - + +
282K ASN* 1.3 86.8 - - - +
284K LEU* 1.3 57.7 + - - +
286K TYR* 3.3 7.2 + - - +
287K LEU* 2.9 29.8 + - - +
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Residues in contact with LEU 284 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272K ILE* 4.2 19.7 - - + +
275K LEU* 3.6 20.8 - - + +
276K VAL* 4.6 2.7 - - + -
280K LYS 3.1 11.5 + - - +
281K ALA 3.2 6.9 + - - +
283K GLU* 1.3 77.9 - - - +
285K PHE* 1.3 58.4 + - - +
287K LEU* 3.2 7.0 + - + -
288K SER* 2.8 35.6 + - - +
304K ALA* 4.6 0.9 - - + +
307K CYS* 3.7 23.3 - - - -
308K TYR* 3.4 39.7 - - + +
311K MET* 3.5 26.0 - - + -
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Residues in contact with PHE 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550F VAL* 3.9 8.1 - - + -
553F SER* 3.7 22.0 - - - -
554F VAL* 3.1 36.8 - - + -
557F LYS* 3.9 19.1 - - - +
281K ALA 2.8 11.8 + - - +
282K ASN 3.7 2.5 - - - +
284K LEU* 1.3 75.1 - - - +
286K TYR* 1.3 63.6 + - - +
288K SER* 4.1 1.5 - - - +
289K HIS* 3.1 56.5 + + - +
308K TYR* 3.3 45.3 - + + -
57M TRP* 4.3 5.6 - + - -
59M ASP* 4.7 3.4 - - + -
60M LEU* 4.0 17.3 - - - -
61M ALA* 4.8 1.8 - - + -
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Residues in contact with TYR 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548F LYS* 5.3 4.0 + - - -
550F VAL* 5.0 7.0 - - + -
551F ALA* 4.2 27.1 - - + +
554F VAL* 3.5 29.2 - - + -
282K ASN 3.0 13.4 + - - +
283K GLU* 3.6 9.4 - - - +
285K PHE* 1.3 79.1 - - - +
287K LEU* 1.3 62.3 + - + +
289K HIS* 4.0 1.0 - - + -
290K LYS* 3.0 67.1 + - + +
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Residues in contact with LEU 287 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258K MET* 3.5 25.8 - - + -
263K PHE* 3.9 24.5 - - + -
268K LEU* 4.8 5.2 - - + -
271K HIS* 3.4 33.9 - - + +
272K ILE* 4.6 16.8 - - + -
275K LEU* 4.5 5.4 - - + -
283K GLU 2.9 15.8 + - - +
284K LEU* 3.2 8.5 + - + +
286K TYR* 1.3 78.3 - - - +
288K SER* 1.3 58.0 + - - +
290K LYS* 3.2 4.0 + - + +
291K LEU* 2.8 35.8 + - + +
304K ALA* 5.9 0.9 - - + -
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Residues in contact with SER 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284K LEU* 2.8 20.8 + - - +
285K PHE* 4.1 3.1 - - - -
287K LEU* 1.3 71.0 - - - +
289K HIS* 1.3 64.5 + - - +
291K LEU* 3.0 4.5 + - - +
292K VAL* 3.0 26.7 + - - +
304K ALA* 2.9 43.8 + - - +
305K VAL* 3.2 10.1 + - - +
308K TYR* 4.0 4.2 - - - +
57M TRP* 3.7 21.5 - - - -
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Residues in contact with HIS 289 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550F VAL* 3.0 37.8 - - + +
285K PHE* 3.1 47.7 + + - +
286K TYR* 4.1 3.4 - - + +
288K SER* 1.3 79.1 - - - +
290K LYS* 1.3 61.8 + - - +
292K VAL* 3.5 5.8 - - + +
293K ASP* 3.4 20.8 + - - +
57M TRP* 3.2 49.0 + + - -
58M THR* 3.8 3.0 + - - -
59M ASP* 3.6 24.5 + - + -
60M LEU* 3.8 5.6 + - - +
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Residues in contact with LYS 290 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548F LYS* 5.0 16.6 - - - +
550F VAL* 4.9 12.3 - - - +
551F ALA* 5.5 0.4 - - - +
54J HIS* 6.3 0.7 - - - +
263K PHE* 3.0 37.0 - - + -
286K TYR* 3.0 60.5 + - + +
287K LEU* 3.6 4.9 - - + +
289K HIS* 1.3 76.5 - - - +
291K LEU* 1.3 62.8 + - - +
293K ASP* 3.4 21.7 - - - +
294K LEU* 3.2 27.1 + - + +
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Residues in contact with LEU 291 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263K PHE* 3.1 33.9 - - + -
268K LEU* 3.8 29.6 - - + -
272K ILE* 4.9 4.0 - - + -
287K LEU* 2.8 22.5 + - + +
288K SER* 3.0 8.5 + - - +
290K LYS* 1.3 75.4 - - - +
292K VAL* 1.3 58.8 + - - +
294K LEU* 4.4 0.4 - - - +
295K TYR* 2.7 45.6 + - + +
300K VAL* 4.2 4.3 - - + -
301K SER* 3.1 32.9 + - - +
304K ALA* 3.9 18.2 - - + -
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Residues in contact with VAL 292 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288K SER 3.0 8.3 + - - -
289K HIS* 3.5 12.6 - - + +
291K LEU* 1.3 72.8 - - - +
293K ASP* 1.3 70.9 - - - +
296K PRO* 3.4 25.7 - - - +
301K SER* 3.1 16.0 + - - +
302K TRP* 3.5 33.7 - - + -
305K VAL* 3.7 22.9 - - + -
55M MET 4.4 4.2 - - - +
57M TRP* 3.5 43.1 - - + +
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Residues in contact with ASP 293 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85J GLU* 5.6 2.3 - - - +
289K HIS 3.4 8.2 + - - +
290K LYS* 3.4 24.8 - - - +
292K VAL* 1.3 86.1 - - - +
294K LEU* 1.3 76.0 + - - +
296K PRO* 3.7 8.0 - - - +
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Residues in contact with LEU 294 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J ALA 5.4 2.3 - - - +
54J HIS* 3.4 39.7 - - + +
83J ALA* 5.7 8.7 - - + -
85J GLU* 6.2 2.0 - - + +
263K PHE* 3.3 37.7 - - + -
290K LYS* 3.2 19.3 + - + +
291K LEU* 4.9 0.4 - - - -
293K ASP* 1.3 96.6 - - - +
295K TYR* 1.3 84.2 + - + +
296K PRO* 3.4 5.3 - - - +
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Residues in contact with TYR 295 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J ALA 4.2 6.7 - - - -
52J GLN* 3.0 66.0 + - + +
53J TYR 5.0 1.1 - - - -
54J HIS* 5.2 2.5 - - + -
55J ARG* 3.6 14.8 + - + +
263K PHE* 4.2 21.1 - + + -
291K LEU* 2.7 31.8 + - + +
294K LEU* 1.3 97.5 - - + +
296K PRO* 1.3 65.2 - - - +
297K SER* 3.1 9.8 + - - +
298K ASN* 3.3 24.1 + - + -
300K VAL* 5.8 2.7 - - + -
301K SER* 3.2 21.9 - - - -
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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