Contacts of the strand formed by residues 177 - 189 (chain 2) in PDB entry 5NER
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 177 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362 TYR* 3.8 22.4 - + - -
822 GLU* 3.9 1.7 - - - +
832 LEU* 3.1 30.6 + - + +
1032 ASN 5.2 2.0 - - - -
1052 TRP* 3.5 31.4 - + + +
1252 MET* 3.7 39.9 - - + -
1262 VAL 3.7 13.5 - - - -
1272 PRO* 3.6 25.8 - - + -
1442 PRO* 5.0 0.2 - - + -
1602 VAL* 3.3 32.8 - - + -
1612 PRO* 3.0 23.7 + - + -
1622 PHE* 4.4 2.2 - + - +
1632 VAL* 3.6 31.9 - - + +
1752 LYS 3.5 3.1 - - - +
1762 PRO* 1.3 90.7 - - + +
1782 THR* 1.3 68.1 + - - +
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Residues in contact with THR 178 (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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1311 ASN* 3.9 11.4 + - - -
1351 LYS* 4.2 4.9 - - + -
802 LEU* 4.2 17.0 - - + -
812 LEU 3.4 17.7 - - - +
822 GLU* 4.2 9.6 - - + +
1242 ALA 3.6 0.5 - - - +
1252 MET* 3.5 6.0 - - - -
1262 VAL* 2.8 42.9 + - - +
1292 LEU* 3.7 39.5 + - + +
1772 TRP* 1.3 80.0 + - - +
1792 LEU* 1.3 63.9 + - - +
1802 VAL 3.7 0.5 + - - -
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Residues in contact with LEU 179 (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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662 LEU* 4.5 7.1 - - + +
792 HIS* 3.2 5.0 - - - +
802 LEU* 3.5 0.3 - - - -
812 LEU* 2.8 61.2 + - + +
832 LEU* 4.2 8.4 - - + +
1072 VAL* 3.7 27.6 - - + -
1092 VAL* 4.0 19.1 - - + -
1232 VAL* 4.9 2.2 - - + -
1242 ALA 3.6 17.7 - - - +
1252 MET* 3.6 25.8 - - + -
1582 ILE* 5.5 2.0 - - + -
1782 THR* 1.3 72.1 - - - +
1802 VAL* 1.3 59.8 + - - +
1812 VAL* 4.2 9.4 + - + +
2012 ALA* 4.3 10.1 - - + -
2032 ILE* 4.5 3.6 - - + -
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Residues in contact with VAL 180 (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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782 CYS* 4.4 17.7 - - + -
792 HIS 3.3 7.9 - - - +
802 LEU* 4.2 21.3 - - + +
1222 LEU 3.6 1.6 - - - +
1232 VAL* 3.4 2.3 - - - -
1242 ALA* 2.9 49.8 + - + +
1262 VAL* 3.6 24.9 - - + -
1292 LEU* 4.8 8.1 - - + -
1322 ILE* 6.2 2.0 - - + -
1372 LEU* 5.5 1.1 - - + -
1402 LEU* 4.0 23.3 - - + -
1782 THR 3.7 0.2 + - - -
1792 LEU* 1.3 74.1 - - - +
1812 VAL* 1.3 66.1 + - - +
1822 MET* 4.8 0.4 - - + +
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Residues in contact with VAL 181 (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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662 LEU* 3.6 27.6 - - + -
672 PHE* 3.5 32.2 - - + -
772 ARG 3.5 4.3 - - - +
782 CYS* 3.6 0.3 - - - -
792 HIS* 3.1 33.2 + - + +
1092 VAL* 4.7 1.8 - - + -
1212 LEU* 4.2 17.5 - - + -
1222 LEU 3.5 2.9 - - - +
1232 VAL* 3.8 29.6 - - + -
1792 LEU* 4.5 9.9 - - + +
1802 VAL* 1.3 79.0 - - - +
1822 MET* 1.3 61.7 + - - +
1992 VAL* 4.5 3.6 - - + -
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Residues in contact with MET 182 (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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752 PHE* 4.2 9.9 - - + -
762 GLY* 4.2 11.4 - - - -
772 ARG 3.3 8.7 - - - +
782 CYS* 4.4 6.7 - - - -
1212 LEU* 3.3 8.4 - - - +
1222 LEU* 2.8 54.9 + - + +
1372 LEU* 3.5 57.9 - - - +
1402 LEU* 4.0 11.9 - - + -
1802 VAL* 4.9 0.9 - - + -
1812 VAL* 1.3 76.0 - - - +
1832 VAL* 1.3 71.3 + - - +
1842 VAL* 3.6 25.1 + - + -
543 PHE* 4.5 2.9 - - + -
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Residues in contact with VAL 183 (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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672 PHE* 4.7 8.5 - - + -
692 TRP* 3.8 32.5 - - + +
732 ASP* 4.1 7.9 - - + +
742 SER 3.9 19.7 - - - +
752 PHE* 3.3 5.9 - - - -
762 GLY 3.0 22.5 + - - -
772 ARG* 3.2 23.6 + - + +
1202 CYS 3.9 3.6 - - - +
1212 LEU* 4.0 7.4 - - + -
1822 MET* 1.3 75.2 - - - +
1842 VAL* 1.3 61.2 + - - +
1852 ALA 3.7 24.9 - - - +
1862 PRO* 3.9 7.4 - - + -
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Residues in contact with VAL 184 (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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752 PHE* 3.7 17.9 - - + -
1202 CYS* 3.0 42.8 + - + +
1222 LEU* 3.7 21.3 - - + +
1472 PHE* 4.5 5.6 - - + -
1822 MET* 3.6 29.8 - - + +
1832 VAL* 1.3 75.2 - - - +
1852 ALA* 1.3 61.6 + - - +
1862 PRO 4.4 0.2 - - - -
543 PHE* 4.0 19.7 - - + -
623 PRO* 3.7 4.8 - - + +
633 TYR* 3.3 22.9 - - - -
2003 VAL* 4.3 12.0 - - + +
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Residues in contact with ALA 185 (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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692 TRP* 3.7 4.2 - - - -
1192 GLY* 3.2 1.2 - - - -
1202 CYS* 3.0 33.8 + - + +
1832 VAL* 3.7 3.3 - - - +
1842 VAL* 1.3 83.1 - - - +
1862 PRO* 1.3 73.7 - - + +
1872 LEU 3.6 0.3 + - - -
633 TYR* 4.1 1.1 - - + -
1123 THR* 3.9 20.0 - - + -
1983 ALA* 3.9 20.4 - - + -
2003 VAL* 4.2 7.4 - - + -
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Residues in contact with PRO 186 (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 THR 4.4 5.8 - - - +
732 ASP 3.3 24.7 - - - +
742 SER* 4.3 10.8 - - - +
752 PHE 5.0 5.2 - - - +
1192 GLY* 3.3 10.9 + - - -
1832 VAL* 3.9 6.4 - - + -
1842 VAL 4.8 0.4 - - - -
1852 ALA* 1.3 90.4 - - + +
1872 LEU* 1.3 69.8 + - - +
1882 THR* 3.7 8.1 + - + +
633 TYR* 3.5 32.3 - - + +
1983 ALA* 5.5 1.3 - - + -
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Residues in contact with LEU 187 (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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692 TRP* 3.2 67.1 - - + +
702 VAL 4.0 10.4 + - - +
712 THR* 3.9 25.4 - - + +
732 ASP 4.5 1.8 + - - -
1172 ASN* 4.0 14.1 - - + +
1182 GLY 3.2 20.2 - - - +
1502 PRO* 5.1 0.2 - - + -
1862 PRO* 1.3 77.8 - - - +
1882 THR* 1.3 76.3 + - - +
1892 VAL* 4.5 3.1 - - + -
1942 ALA 4.6 1.6 - - - +
1952 PRO 4.1 18.6 - - - +
1962 GLN* 4.3 2.0 - - - -
1972 ILE* 3.6 13.9 - - + -
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Residues in contact with THR 188 (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 THR* 4.6 0.4 - - - -
1172 ASN* 2.8 27.0 + - - +
1182 GLY* 2.7 35.3 + - - -
1192 GLY 4.9 0.4 - - - +
1862 PRO* 3.7 11.0 + - + +
1872 LEU* 1.3 83.3 - - - +
1892 VAL* 1.3 64.3 + - - +
1902 ASN* 3.6 23.3 + - - +
1143 PRO* 4.8 1.6 - - - +
1963 GLY 4.6 15.3 - - - +
1973 ASP* 5.3 5.1 + - - +
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Residues in contact with VAL 189 (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 THR* 3.8 19.6 - - + +
1172 ASN* 3.6 6.7 - - - +
1872 LEU* 4.5 2.7 - - + -
1882 THR* 1.3 75.3 - - - +
1902 ASN* 1.3 68.2 + - - +
1912 THR 5.3 0.2 - - - -
1932 GLY* 4.3 12.1 - - - +
1942 ALA 3.0 28.7 - - - +
1952 PRO* 3.1 23.3 - - + +
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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