Contacts of the helix formed by residues 135 - 143 (chain 2) 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 ARG 135 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1921 LEU* 3.8 31.8 - - + +
1931 ALA 2.4 30.6 + - - -
1941 ILE* 3.3 3.8 + - - +
1951 HIS* 3.3 42.2 + - + +
1332 GLN* 3.2 8.8 - - + +
1342 LYS* 1.3 80.5 - - + +
1362 GLU* 1.3 59.8 + - - +
1372 LEU 3.2 1.2 + - - -
1382 TYR* 3.8 14.7 + - + +
873 SER* 4.4 6.3 + - - -
883 ASN* 2.5 40.0 + - - +
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Residues in contact with GLU 136 (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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1891 ARG* 5.9 0.2 + - - -
1901 PRO* 3.2 34.3 - - + +
1921 LEU* 4.5 18.8 - - + +
1292 LEU* 5.1 6.4 - - - +
1322 ILE* 3.3 31.8 - - + +
1332 GLN* 3.4 33.4 + - - +
1342 LYS 3.3 0.2 - - - -
1352 ARG* 1.3 74.8 - - - +
1372 LEU* 1.3 68.6 + - - +
1382 TYR 3.2 4.0 + - - -
1392 GLN* 3.4 17.4 + - - +
1402 LEU* 4.2 14.2 + - - +
1432 PHE* 4.7 2.1 - - - -
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Residues in contact with LEU 137 (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* 4.4 6.6 - - + -
762 GLY* 3.8 35.2 - - - +
782 CYS* 5.0 9.2 - - + -
1322 ILE* 4.0 25.8 - - + -
1332 GLN 3.5 10.3 - - - +
1342 LYS* 3.6 27.4 - - + +
1352 ARG 3.2 1.4 - - - -
1362 GLU* 1.3 80.4 - - - +
1382 TYR* 1.3 65.0 + - - +
1392 GLN 3.2 1.3 + - - -
1402 LEU* 3.5 25.8 + - + +
1822 MET* 3.7 31.3 - - + +
543 PHE* 4.1 7.1 - - - -
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Residues in contact with TYR 138 (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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1921 LEU* 6.3 0.2 - - + -
752 PHE* 3.5 34.3 - + - -
1342 LYS* 4.9 7.6 + - - -
1352 ARG* 4.0 10.1 - - + +
1362 GLU 3.2 1.0 - - - -
1372 LEU* 1.3 78.4 - - - +
1392 GLN* 1.3 50.1 + - - +
1402 LEU 3.6 0.4 - - - -
533 THR* 2.6 22.9 - - - +
543 PHE* 2.9 34.5 + - + +
553 LEU 4.2 19.3 - - - -
563 HIS* 3.4 13.2 + + - -
603 ASP* 2.4 39.3 + - - +
613 VAL 4.7 0.4 - - - -
623 PRO* 4.2 4.9 - - + -
883 ASN* 2.4 70.2 - - + +
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Residues in contact with GLN 139 (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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1901 PRO* 3.4 27.2 - - + +
1911 LEU 2.9 37.9 + - - +
1921 LEU* 4.5 4.6 - - + +
1362 GLU 3.4 9.0 + - - +
1372 LEU 3.2 0.8 - - - -
1382 TYR* 1.3 74.5 - - - +
1402 LEU* 1.3 56.7 + - - +
1412 THR 3.2 6.0 + - - -
1422 LEU* 4.0 13.7 + - + +
1432 PHE* 4.3 2.1 - - - -
533 THR* 2.5 35.9 - - + +
883 ASN 3.1 13.3 + - - +
893 THR 2.2 12.9 + - - -
903 PHE* 1.8 54.2 - - + +
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Residues in contact with LEU 140 (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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1222 LEU* 3.8 25.8 - - + -
1242 ALA* 4.1 14.7 - - + +
1262 VAL* 5.0 7.0 - - + -
1292 LEU* 5.4 4.9 - - + -
1362 GLU* 4.2 11.2 + - - +
1372 LEU* 3.5 24.5 + - + +
1382 TYR 3.6 1.0 - - - -
1392 GLN* 1.3 73.8 - - - +
1412 THR* 1.3 63.3 + - - +
1422 LEU 3.2 4.2 + - - -
1432 PHE* 3.4 39.8 + - + +
1452 HIS* 4.5 3.1 - - - +
1802 VAL* 3.8 27.6 - - + -
1822 MET* 3.6 27.8 - - + -
543 PHE* 5.1 0.6 - - + -
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Residues in contact with THR 141 (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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1222 LEU* 4.2 3.8 - - - +
1392 GLN 3.2 0.8 - - - -
1402 LEU* 1.3 77.2 - - - +
1422 LEU* 1.3 62.0 + - - +
1432 PHE 3.1 0.6 - - - +
1452 HIS* 2.9 54.1 + - + +
1472 PHE* 4.9 1.1 - - + -
513 CYS* 4.1 5.6 - - - +
523 PRO* 2.2 46.5 + - + +
533 THR* 4.0 5.6 - - - -
543 PHE* 3.6 28.6 - - - -
2023 LEU* 4.4 6.9 - - + +
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Residues in contact with LEU 142 (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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1881 PRO* 4.6 13.6 - - + +
1891 ARG* 3.5 33.0 - - - +
1901 PRO* 3.8 11.9 - - + -
362 TYR* 4.6 3.7 + - - -
1392 GLN* 4.0 11.7 - - - +
1402 LEU 3.2 1.0 - - - -
1412 THR* 1.3 77.4 - - - +
1432 PHE* 1.3 64.3 + - + +
1442 PRO* 4.8 0.3 - - - +
473 VAL* 3.7 24.0 - - + +
513 CYS* 3.4 45.4 - - + +
533 THR* 4.3 6.5 - - - +
903 PHE* 3.9 26.2 - - + -
684 PHE* 4.5 11.3 - - - -
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Residues in contact with PHE 143 (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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1881 PRO 3.3 19.1 - - - -
1891 ARG* 3.6 15.9 - - - -
1901 PRO* 3.6 32.1 - - + -
362 TYR* 3.8 15.5 - - - -
1242 ALA* 4.6 3.6 - - + -
1252 MET 3.6 10.3 - - - +
1262 VAL* 3.6 31.6 - - + -
1272 PRO* 4.2 7.2 - - + -
1292 LEU* 5.4 1.6 - - + -
1362 GLU* 4.7 3.6 - - - -
1392 GLN 4.3 5.8 - - - -
1402 LEU* 3.4 42.4 - - + +
1412 THR 3.1 11.3 - - - +
1422 LEU* 1.3 82.9 - - + +
1442 PRO* 1.4 73.0 - - + +
1452 HIS* 3.0 12.1 + - - +
513 CYS* 5.4 0.3 - - - -
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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