Contacts of the strand formed by residues 118 - 126 (chain 3) in PDB entry 5NEU
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 118 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512 ARG* 5.5 3.5 - - - +
1113 PHE* 5.4 0.4 - - - -
1153 THR 4.9 12.6 + - - +
1163 ASP 3.7 8.0 + - - +
1173 ALA* 1.3 79.4 - - - +
1193 ALA* 1.3 60.3 + - - +
1493 THR* 3.6 23.5 + - - +
1503 GLY* 5.1 5.3 - - - -
1913 HIS* 3.4 0.7 - - - +
1923 GLY* 2.4 44.0 + - - +
1943 ALA* 4.2 1.8 - - - +
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Residues in contact with ALA 119 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663 THR* 5.3 0.4 - - + -
1113 PHE* 4.8 3.6 - - + -
1183 LYS* 1.3 77.2 - - - +
1203 ARG* 1.3 61.9 + - - +
1213 TYR* 3.9 26.5 - - + +
1483 ASP* 3.6 2.4 - - - +
1493 THR* 3.1 37.2 + - + +
1903 THR* 3.5 16.2 - - - +
1913 HIS* 3.7 13.2 - - + +
1943 ALA* 4.5 6.3 - - + -
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Residues in contact with ARG 120 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193 ALA* 1.3 75.4 - - - +
1213 TYR* 1.3 68.8 + - - +
1463 GLU* 3.3 39.9 + - - +
1473 TRP* 3.4 18.9 + - - +
1483 ASP* 3.7 26.8 + - + +
1893 ILE* 3.0 38.2 + - + +
1903 THR* 3.2 29.8 + - + +
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Residues in contact with TYR 121 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663 THR* 3.5 15.9 - - - +
743 LEU* 3.8 9.6 - - + -
1113 PHE* 3.4 28.6 - + - -
1193 ALA* 3.9 16.5 - - + +
1203 ARG* 1.3 84.4 - - - +
1223 MET* 1.3 64.3 + - - +
1463 GLU* 3.4 22.3 - - - +
1473 TRP* 3.0 52.2 + + + -
1493 THR* 4.5 8.7 - - + -
1863 LEU* 5.9 0.4 - - + -
1873 PHE 3.6 9.4 - - - +
1883 GLN* 3.6 31.4 - - + +
1893 ILE* 3.9 6.5 - - - +
1993 LEU* 3.6 36.7 - - + +
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Residues in contact with MET 122 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1213 TYR* 1.3 77.5 - - - +
1233 ILE* 1.3 60.2 + - - +
1243 ALA* 4.4 4.7 - - + -
1363 PRO* 3.8 31.9 - - - +
1393 ALA* 3.5 33.0 - - + +
1403 ALA* 4.6 1.8 - - - -
1443 HIS* 3.6 31.0 - - + +
1453 ALA 3.3 12.8 - - - +
1463 GLU* 3.7 12.8 - - + +
1473 TRP* 4.0 4.6 - - - -
1863 LEU* 3.2 4.2 - - - +
1873 PHE* 2.8 50.9 + - + +
1893 ILE* 4.0 15.0 - - + -
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Residues in contact with ILE 123 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073 LEU* 3.7 20.4 - - + -
1093 PHE* 3.6 32.5 - - + -
1223 MET* 1.3 75.0 - - - +
1243 ALA* 1.3 62.3 + - - +
1443 HIS* 3.3 3.4 - - - -
1453 ALA* 3.1 29.6 + - + +
1473 TRP* 3.6 20.6 - - + -
1573 PHE* 3.9 41.4 - - + -
1843 VAL* 3.8 16.2 - - + -
1853 CYS 3.3 11.4 - - - +
1863 LEU* 4.1 10.3 - - + -
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Residues in contact with ALA 124 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223 MET* 4.4 2.5 - - + -
1233 ILE* 1.3 75.7 - - - +
1253 TYR* 1.3 60.6 + - - +
1263 ALA 4.0 0.6 + - - -
1333 PRO* 5.7 0.7 - - + -
1393 ALA* 3.8 22.2 - - + +
1423 CYS* 3.8 17.5 - - + -
1433 ILE 4.1 0.4 - - - -
1443 HIS* 3.7 22.4 - - + +
1573 PHE* 5.4 1.1 - - - -
1843 VAL* 3.5 6.0 - - - +
1853 CYS* 2.7 37.0 + - + +
1873 PHE* 4.9 2.6 - - + -
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Residues in contact with TYR 125 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793 LEU* 3.7 30.7 - - + -
1243 ALA* 1.3 72.6 - - - +
1263 ALA* 1.3 59.0 + - - +
1273 PRO* 3.3 33.0 - - + +
1283 PRO* 4.5 1.4 - - - +
1423 CYS* 3.3 16.4 - - - +
1433 ILE* 3.7 24.4 + - + +
1573 PHE* 5.3 0.9 - - + -
1593 ILE* 4.2 17.3 - - + -
1603 PRO* 4.1 30.5 + - + -
1623 LEU* 3.9 42.6 + - + +
1813 GLN* 3.4 23.7 + - - -
1823 GLY* 4.3 4.9 - - - -
1833 TRP 3.5 15.9 - - - -
1843 VAL* 4.6 2.5 - - + +
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Residues in contact with ALA 126 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243 ALA 4.0 2.0 + - - -
1253 TYR* 1.3 74.0 - - - +
1273 PRO* 1.3 69.4 - - + +
1313 GLU 5.7 0.4 - - - +
1323 PRO* 4.6 4.0 - - + -
1333 PRO* 3.7 30.5 - - + -
1423 CYS* 4.2 9.0 - - - -
1823 GLY* 3.8 0.5 - - - -
1833 TRP* 3.0 47.5 + - + +
1853 CYS* 4.9 3.3 - - - +
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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
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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