Contacts of the helix formed by residues 220 - 241 (chain 0) in PDB entry 4BOG
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 TYR 220 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2190 PHE* 1.3 92.7 - + + +
2210 ILE* 1.3 60.4 + - + +
2220 VAL 2.7 11.2 + - - -
2230 TYR* 2.8 44.9 + + + +
2240 THR* 2.9 24.7 + - - +
2730 THR* 6.3 3.6 - - + -
2791 PRO* 2.8 40.7 + - + +
2821 ALA* 3.8 4.0 - - + +
2831 LEU* 3.1 43.5 + - + +
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Residues in contact with ILE 221 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1350 PHE* 6.0 6.7 - - + -
2170 PRO 3.9 6.5 - - - +
2180 LEU* 3.0 51.4 - - + -
2190 PHE 3.9 2.9 - - - +
2200 TYR* 1.3 74.5 - - + +
2220 VAL* 1.3 55.4 + - - +
2240 THR* 3.2 16.6 - - + +
2250 ILE* 2.9 34.7 + - + +
2830 TYR* 4.9 25.1 - - + -
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Residues in contact with VAL 222 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2180 LEU* 3.5 28.7 - - + +
2190 PHE* 2.9 24.7 - - - +
2200 TYR 2.7 0.8 - - - -
2210 ILE* 1.3 78.0 - - - +
2230 TYR* 1.3 63.3 + - + +
2250 ILE* 3.2 27.7 + - + +
2260 VAL* 3.3 9.9 + - + +
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Residues in contact with TYR 223 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2190 PHE 4.6 2.7 - - - -
2200 TYR* 2.8 70.2 + + + +
2220 VAL* 1.3 80.8 - - + +
2240 THR* 1.3 56.6 + - - +
2260 VAL* 2.6 21.7 - - + +
2270 PRO* 2.3 33.7 - - + +
2660 LEU* 5.9 2.2 - - + -
2690 LYS* 5.2 11.5 + - - +
2751 SER* 5.3 7.4 - - - -
2761 GLN* 4.1 29.7 + - - -
2791 PRO* 4.1 14.1 - - + +
2961 MET* 6.0 13.0 - - + -
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Residues in contact with THR 224 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2200 TYR* 2.9 18.8 + - - +
2210 ILE* 3.2 23.6 - - + +
2230 TYR* 1.3 78.3 - - - +
2250 ILE* 1.3 56.8 + - + +
2270 PRO* 2.5 35.7 - - + +
2280 CYS* 3.2 16.6 + - - +
2660 LEU* 6.4 0.2 - - + -
2690 LYS* 3.8 24.0 + - - +
2870 ILE* 6.0 7.0 - - + -
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Residues in contact with ILE 225 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2210 ILE 2.9 15.0 + - - +
2220 VAL* 3.2 16.4 - - + +
2240 THR* 1.3 75.1 - - + +
2260 VAL* 1.3 73.1 + - + +
2280 CYS* 3.1 9.5 + - + +
2290 ILE* 2.8 48.4 + - + +
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Residues in contact with VAL 226 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2220 VAL* 3.3 13.0 + - + +
2230 TYR* 2.6 38.8 - - + +
2250 ILE* 1.3 83.7 - - + +
2270 PRO* 1.3 58.6 - - + +
2290 ILE* 4.6 1.8 - - - -
2300 LEU* 2.3 75.5 + - + +
3001 THR* 5.5 7.0 - - + +
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Residues in contact with PRO 227 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2230 TYR* 2.3 33.7 - - + +
2240 THR* 2.5 29.4 - - + +
2260 VAL* 1.3 75.2 - - + +
2280 CYS* 1.3 64.3 + - - +
2300 LEU* 4.5 1.8 - - + -
2310 ILE* 2.4 57.2 + - + +
2660 LEU* 4.1 29.4 - - + -
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Residues in contact with CYS 228 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2240 THR* 3.2 16.7 + - - +
2250 ILE* 3.1 11.4 + - - +
2270 PRO* 1.3 81.5 - - - +
2290 ILE* 1.3 55.2 + - + +
2310 ILE* 4.0 4.3 - - - +
2320 SER* 2.5 31.8 + - - -
2630 LEU* 6.4 2.2 - - - -
2870 ILE* 5.1 18.8 - - - -
2900 LEU* 5.2 15.9 - - + -
2940 SER* 5.3 2.1 + - - -
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Residues in contact with ILE 229 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2250 ILE* 2.8 45.2 + - + +
2260 VAL* 4.0 3.1 - - - +
2270 PRO 2.8 1.2 + - - -
2280 CYS* 1.3 72.6 - - + +
2300 LEU* 1.3 59.1 + - + +
2310 ILE 3.3 1.1 - - - -
2320 SER* 2.8 12.4 - - - -
2330 ILE* 2.7 32.8 + - + +
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Residues in contact with LEU 230 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2260 VAL* 2.3 74.8 + - + +
2270 PRO* 4.4 2.2 - - + -
2290 ILE* 1.3 68.9 - - + +
2310 ILE* 1.3 57.7 - - + +
2320 SER 2.9 1.3 - - - -
2330 ILE* 2.7 56.9 + - + +
2340 LEU* 3.1 11.5 + - + +
3001 THR* 5.0 18.8 - - + +
3031 VAL* 4.2 28.0 - - + -
3041 VAL* 5.6 3.8 - - + -
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Residues in contact with ILE 231 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2270 PRO* 2.4 62.3 + - + +
2280 CYS* 3.9 4.3 - - - +
2300 LEU* 1.3 70.2 - - + +
2320 SER* 1.3 49.5 - - - +
2340 LEU* 3.2 13.0 + - + +
2350 ALA* 2.6 32.1 + - + +
2590 LEU* 3.2 38.7 - - + +
2620 PHE* 4.7 26.2 - - + -
2630 LEU* 4.0 12.1 - - + -
2660 LEU* 5.3 4.7 - - + -
2940 SER* 5.4 5.2 - - - +
2721 LEU* 5.6 4.5 - - + -
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Residues in contact with SER 232 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2280 CYS 2.5 19.2 + - - -
2290 ILE* 2.8 19.4 - - - -
2310 ILE* 1.3 79.9 - - - +
2330 ILE* 1.4 57.8 + - - -
2350 ALA* 3.3 10.6 - - - +
2360 ILE* 2.4 40.1 + - - +
2940 SER* 4.8 6.8 + - - -
4460 MET* 4.8 16.7 - - - +
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Residues in contact with ILE 233 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2290 ILE* 2.7 14.9 + - + +
2300 LEU* 2.7 66.6 + - + +
2320 SER* 1.4 69.1 - - - +
2340 LEU* 1.3 52.6 + - + +
2360 ILE* 3.1 10.5 - - + +
2370 LEU* 2.6 58.1 + - + +
3031 VAL* 5.6 3.8 - - + +
3041 VAL* 5.4 15.5 - - + +
3071 GLY* 4.4 13.0 - - - -
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Residues in contact with LEU 234 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2300 LEU 3.1 13.6 + - - +
2310 ILE* 3.8 11.9 - - + +
2330 ILE* 1.3 80.4 - - + +
2350 ALA* 1.3 53.0 - - - +
2370 LEU* 2.9 14.8 - - + +
2380 VAL* 2.5 44.2 + - + +
2550 ALA* 6.0 4.0 - - + +
2580 ALA* 6.2 0.2 - - + -
2590 LEU* 4.9 12.8 - - + +
2620 PHE* 4.9 20.0 - - + -
2641 LEU* 3.9 19.1 - - + -
2651 LEU* 5.3 8.3 - - + -
2681 ALA* 4.9 5.4 - - + -
3031 VAL* 5.5 7.6 - - + +
3061 CYS* 5.7 0.9 - - + -
3071 GLY* 4.5 6.7 - - - +
3101 LEU* 3.8 25.4 - - + -
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Residues in contact with ALA 235 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2310 ILE 2.6 22.3 + - - +
2320 SER* 2.8 15.0 + - - +
2340 LEU* 1.3 68.8 - - - +
2360 ILE* 1.3 52.4 + - - +
2370 LEU 2.7 3.6 - - - -
2380 VAL* 2.6 23.1 + - - -
2390 PHE* 2.6 49.5 + - + -
2590 LEU* 4.3 12.1 - - + +
2940 SER* 4.8 10.1 - - - +
4460 MET* 5.9 0.4 - - - -
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Residues in contact with ILE 236 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2320 SER* 2.4 42.2 + - - +
2330 ILE* 3.1 15.9 - - + +
2350 ALA* 1.3 69.8 - - - +
2370 LEU* 1.3 53.0 + - + +
2390 PHE* 3.1 15.2 - - + +
2400 TYR* 2.5 62.1 + - + +
4390 PHE* 4.8 15.5 - - + -
4420 ILE* 5.7 0.7 - - + -
4460 MET* 3.7 29.5 - - + -
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Residues in contact with LEU 237 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2330 ILE* 2.6 47.7 + - + +
2340 LEU* 2.9 17.7 - - + +
2360 ILE* 1.3 79.0 - - + +
2380 VAL* 1.3 51.7 + - + +
2390 PHE 3.1 4.0 - - - -
2400 TYR* 3.8 6.5 - - + -
2410 LEU* 2.3 43.3 + - + +
3071 GLY* 3.9 9.0 - - - +
3101 LEU* 3.2 44.0 - - + -
3111 ASN* 3.7 24.9 - - - +
3141 PHE* 4.3 3.0 - - + -
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Residues in contact with VAL 238 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2340 LEU* 2.5 30.1 + - + +
2350 ALA* 2.6 7.9 + - - +
2370 LEU* 1.3 73.4 - - + +
2390 PHE* 1.3 67.6 + - + +
2410 LEU* 4.0 4.7 - - + -
2420 PRO* 2.8 22.8 - - - +
2480 LYS* 2.7 31.8 + - - +
2520 SER* 4.6 6.3 - - - +
2550 ALA* 3.2 33.2 - - + -
2560 LEU* 4.8 14.4 - - + -
2590 LEU* 5.4 2.5 - - + -
3010 VAL* 5.2 1.8 - - + -
3050 HIS* 4.1 15.4 + - + +
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Residues in contact with PHE 239 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2350 ALA* 2.6 52.5 - - + -
2360 ILE* 3.1 12.3 - - - +
2380 VAL* 1.3 96.1 - - + +
2400 TYR* 1.3 57.7 + - - +
2420 PRO* 2.9 22.9 - - - +
2430 PRO* 3.8 1.2 - - - +
2560 LEU* 5.1 0.7 - - + -
2590 LEU* 5.1 1.6 - - + -
2940 SER* 5.5 4.5 - - - -
2970 LEU* 4.9 9.9 - - + -
2980 SER* 4.4 18.6 - - - -
3010 VAL* 4.3 27.6 - - + -
3050 HIS* 5.9 0.4 - - - -
4390 PHE* 3.6 21.4 - - - +
4420 ILE* 3.9 36.3 - - + -
4460 MET* 4.4 11.7 - - + -
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Residues in contact with TYR 240 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2360 ILE* 2.5 41.4 + - + +
2370 LEU* 3.5 9.4 - - + +
2390 PHE* 1.3 74.8 - - - +
2410 LEU* 1.3 56.3 + - - +
2420 PRO* 3.2 2.4 - - - -
2430 PRO* 3.4 9.0 - - + +
2440 ASP* 2.8 50.6 + - + +
4390 PHE* 4.6 28.0 - + + -
3111 ASN* 4.3 18.1 + - - +
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Residues in contact with LEU 241 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2370 LEU 2.3 30.8 + - - +
2380 VAL* 4.8 4.9 - - + -
2400 TYR* 1.3 68.0 - - - +
2420 PRO* 1.4 56.6 - - - +
2440 ASP* 3.4 5.8 - - - -
2450 ALA* 2.4 46.3 + - + -
2480 LYS* 3.2 34.5 - - + +
2510 LEU* 3.2 40.8 - - + -
3101 LEU* 5.0 6.7 - - + -
3141 PHE* 2.9 56.5 - - + -
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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