Contacts of the strand formed by residues 226 - 238 (chain 2) in PDB entry 3EPD
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 TRP 226 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2101 ASP* 5.4 0.4 - - - -
342 ALA* 4.2 7.2 - - + -
352 TYR* 3.9 23.1 - + - -
812 LYS* 3.5 5.8 - - - +
822 LEU* 2.8 39.4 + - + +
1042 SER 5.6 0.2 - - - -
1062 TYR* 4.3 16.2 - + - -
1262 ALA* 3.6 29.6 - - + -
1272 ILE 3.4 28.5 - - - -
1282 PRO* 3.6 15.0 - - + -
1302 TYR* 5.0 2.5 - - - -
1932 PRO* 4.1 3.4 - - + -
2092 LEU* 3.9 37.2 - - + +
2102 PRO* 3.0 33.0 + - + -
2112 TYR* 4.5 1.5 - - - +
2122 VAL* 3.6 25.0 - - + +
2242 ASN* 4.5 1.8 - - - +
2252 ASN* 1.3 92.5 - - + +
2272 GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 227 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802 TRP 3.4 10.8 - - - -
812 LYS* 3.9 11.9 - - - -
1252 PHE 3.7 0.7 - - - +
1262 ALA* 3.4 4.7 - - - -
1272 ILE* 2.9 35.0 + - - -
1302 TYR* 3.9 17.5 - - - +
2262 TRP* 1.3 75.2 - - - +
2282 ILE* 1.3 63.6 + - - +
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Residues in contact with ILE 228 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792 TRP* 3.2 7.5 - - - +
802 TRP* 2.9 48.0 + - + +
822 LEU* 4.1 25.4 - - + -
1082 VAL* 4.1 34.8 - - + -
1102 VAL* 5.3 0.9 - - + -
1242 VAL* 4.6 12.1 - - + -
1252 PHE 3.4 5.6 - - - +
1262 ALA* 4.3 10.3 - - + -
1302 TYR* 5.0 0.7 - - - -
2072 ILE* 6.2 1.6 - - + -
2092 LEU* 4.2 11.0 - - + -
2262 TRP* 5.2 0.4 - - + -
2272 GLY* 1.3 80.1 - - - +
2292 ALA* 1.3 60.5 + - - +
2302 ILE* 4.4 20.2 - - + -
2502 VAL* 5.6 3.8 - - + -
2522 ILE* 5.1 5.8 - - + -
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Residues in contact with ALA 229 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782 TRP 3.6 4.9 - - - -
792 TRP* 4.4 0.9 - - - +
1232 GLY 3.4 4.0 - - - +
1242 VAL* 3.6 1.6 - - - -
1252 PHE* 3.0 38.3 + - + +
1272 ILE* 4.3 9.9 - - + -
1302 TYR* 4.0 27.4 - - + +
1562 PHE* 4.2 4.0 - - + -
1802 LEU* 4.8 1.6 - - + -
2272 GLY 4.1 0.2 - - - -
2282 ILE* 1.3 72.5 - - - +
2302 ILE* 1.3 62.0 + - - +
2312 LEU* 4.0 17.9 - - + -
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Residues in contact with ILE 230 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772 GLY* 3.2 3.5 - - - -
782 TRP* 2.9 49.7 + - + +
802 TRP* 3.7 27.8 - - + -
1102 VAL* 3.8 29.6 - - + -
1222 LEU* 3.9 34.3 - - + -
1232 GLY 3.2 7.9 - - - +
1242 VAL* 4.4 11.4 - - + -
2282 ILE* 4.4 11.0 - - + -
2292 ALA* 1.3 75.6 - - - +
2312 LEU* 1.3 64.3 + - - +
2482 ILE* 4.4 6.7 - - + -
2502 VAL* 4.1 9.6 - - + -
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Residues in contact with LEU 231 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762 LYS 3.9 14.4 - - - +
772 GLY* 4.2 0.2 - - - -
1222 LEU* 3.5 4.6 - - - -
1232 GLY* 2.9 31.4 + - - +
1252 PHE* 4.2 10.1 - - + -
1562 PHE* 4.1 21.8 - - + -
1772 ASP* 3.9 32.1 - - + +
1802 LEU* 4.3 3.1 - - + -
1862 LEU* 3.9 27.1 - - + -
2292 ALA* 4.0 22.7 - - + -
2302 ILE* 1.3 79.6 - - - +
2322 PRO* 1.3 65.5 - - + +
2332 LEU* 3.1 10.7 + - + +
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Residues in contact with PRO 232 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712 TRP* 3.9 27.4 - - + +
752 SER 3.5 23.3 - - - +
762 LYS* 3.5 22.4 - - - +
772 GLY* 4.0 2.0 - - - +
782 TRP* 4.5 9.9 - - + -
1212 ALA 3.6 6.5 - - - +
1222 LEU* 4.2 4.5 - - + -
2312 LEU* 1.3 82.1 - - + +
2332 LEU* 1.3 65.1 + - - +
2342 SER* 3.2 10.3 + - - +
2352 PRO* 4.5 10.0 - - + +
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Residues in contact with LEU 233 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212 ALA* 2.8 14.5 + - + +
1232 GLY* 3.7 28.5 - - - +
1252 PHE* 4.6 9.0 - - + -
1862 LEU* 3.9 27.8 - - + -
1902 PHE* 3.8 26.5 - - + -
1962 ILE* 4.2 20.0 - - + -
2312 LEU* 3.1 10.2 + - + +
2322 PRO* 1.3 73.0 - - - +
2342 SER* 1.3 59.8 + - - +
2352 PRO* 4.5 1.6 - - - +
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Residues in contact with SER 234 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712 TRP* 3.8 4.7 - - - -
1202 GLY* 3.4 3.9 - - - -
1212 ALA* 3.0 44.7 + - - +
2322 PRO* 4.2 2.8 - - - +
2332 LEU* 1.3 80.2 - - - +
2352 PRO* 1.3 73.6 + - - +
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Residues in contact with PRO 235 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712 TRP* 4.9 0.4 - - - +
732 LYS* 4.6 15.5 - - + +
1192 GLN* 3.7 2.4 + - - +
1202 GLY* 3.6 9.0 + - - -
2322 PRO* 4.5 13.2 - - + +
2332 LEU 4.5 2.2 - - - +
2342 SER* 1.3 93.9 + - - +
2362 LEU* 1.3 67.4 + - - +
2372 ASP* 3.5 5.2 + - + +
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Residues in contact with LEU 236 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712 TRP* 3.3 56.5 - - + +
722 GLY* 4.3 6.7 + - - -
732 LYS* 3.4 24.9 - - - +
1182 HIS* 4.4 9.2 - - + -
1192 GLN 3.5 12.1 - - - +
1992 LEU* 4.1 9.9 - - + -
2352 PRO* 1.3 77.0 - - - +
2372 ASP* 1.3 72.0 + - - +
2442 VAL* 3.8 32.8 - - + +
2462 ILE* 3.9 32.3 - - + +
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Residues in contact with ASP 237 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732 LYS* 3.0 26.0 + - - +
1172 PHE 4.4 0.2 - - - +
1182 HIS* 3.5 4.7 - - - +
1192 GLN* 3.0 59.8 + - + +
2352 PRO 4.4 2.9 - - - +
2362 LEU* 1.3 77.3 - - - +
2382 PHE* 1.3 76.6 + - - +
2392 ALA 4.7 3.3 - - - +
2402 GLN* 5.5 1.2 - - - -
2412 ASP 4.0 1.0 - - - +
2442 VAL* 4.2 2.5 - - - -
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Residues in contact with PHE 238 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1152 SER* 4.4 1.8 - - - -
1172 PHE* 3.6 25.8 - - + -
1182 HIS* 3.4 39.7 - + + -
2372 ASP* 1.3 82.3 + - - +
2392 ALA* 1.4 90.0 + - + +
2402 GLN* 2.9 4.7 + - - -
2412 ASP* 3.1 41.7 + - - +
2442 VAL* 3.6 29.7 - - + +
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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