Contacts of the helix formed by residues 134 - 142 (chain 2) in PDB entry 3TDD
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 ILE 134 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32 ILE 6.1 0.2 - - - +
1262 ILE* 4.3 12.8 - - + -
1302 GLY 4.0 0.9 - - - +
1312 SER* 3.3 22.2 - - - +
1332 PHE* 1.3 82.2 - - - +
1352 TYR* 1.3 66.5 + - - +
1362 GLY 3.3 1.6 - - - -
1372 TYR* 3.9 10.3 - - + -
1382 CYS* 2.9 43.7 + - - -
1582 SER* 3.2 37.9 - - - +
1592 LEU* 4.5 9.0 - - + -
1612 GLN* 3.6 13.5 - - + -
1622 ALA* 3.6 27.4 - - + +
136N GLY* 4.7 2.0 - - - -
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Residues in contact with TYR 135 (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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251 LEU* 3.7 23.6 - - + +
271 ARG* 3.3 38.7 + - + -
1242 TYR* 5.0 0.3 + - - -
1262 ILE* 3.8 25.4 + - + -
1312 SER* 3.1 42.7 + - - -
1322 THR* 3.6 19.9 + - + +
1332 PHE 3.5 2.2 - - - -
1342 ILE* 1.3 76.8 - - - +
1362 GLY* 1.3 65.3 + - - +
1382 CYS* 4.0 0.7 - - - +
1392 ASP* 3.1 26.0 + - - +
133N PHE* 4.2 11.0 - + + -
165N TRP* 3.6 55.0 + + + -
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Residues in contact with GLY 136 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1352 TYR* 1.3 80.0 - - - +
1372 TYR* 1.3 62.2 + - - +
1402 LYS* 3.1 28.2 + - - +
133N PHE 3.0 19.7 + - - -
134N ILE* 4.7 0.2 - - - -
137N TYR* 4.3 7.2 - - - -
161N GLN* 2.9 30.6 + - - +
165N TRP* 4.0 1.3 - - - +
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Residues in contact with TYR 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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1342 ILE* 3.5 15.3 + - + +
1352 TYR 3.3 0.4 - - - -
1362 GLY* 1.3 74.9 - - - +
1382 CYS* 1.3 63.9 + - - +
1402 LYS 3.2 1.6 + - - -
1412 ASN* 2.9 61.9 + - + +
1542 PHE* 4.5 5.5 - + - -
1572 HIS* 3.3 27.9 - - + +
1582 SER* 3.5 38.8 - - - -
1612 GLN* 5.3 2.2 - - + -
133N PHE 4.5 0.2 + - - -
136N GLY* 4.3 3.8 - - - -
137N TYR* 3.9 34.7 - + - +
140N LYS* 3.6 41.5 - - + -
141N ASN* 5.1 2.0 - - - -
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Residues in contact with CYS 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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42 MET* 4.2 0.7 - - - -
1242 TYR* 3.3 22.9 - - + +
1262 ILE* 4.1 19.1 - - + -
1342 ILE* 2.9 40.9 + - - +
1352 TYR* 4.1 1.6 - - - +
1372 TYR* 1.3 73.7 - - - +
1392 ASP* 1.3 57.8 + - - +
1422 PHE* 2.8 35.5 + - - +
1542 PHE* 3.8 14.1 - - + -
1582 SER* 3.3 31.6 - - - -
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Residues in contact with ASP 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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1242 TYR* 3.5 9.6 + - - +
1352 TYR 3.1 18.4 + - - +
1382 CYS* 1.3 77.6 - - - +
1402 LYS* 1.3 61.7 + - - +
1412 ASN 3.8 0.2 + - - -
1422 PHE* 4.4 6.7 + - - +
161N GLN* 2.8 26.7 - - - +
164N LYS* 2.7 33.2 + - - -
165N TRP* 3.8 20.7 - - + -
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Residues in contact with LYS 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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1362 GLY 3.1 17.5 + - - +
1372 TYR 3.8 0.4 - - - +
1382 CYS 3.1 0.2 - - - -
1392 ASP* 1.3 80.6 - - - +
1412 ASN* 1.3 69.5 + - - +
1422 PHE 3.8 1.8 - - - +
18N LEU* 3.0 28.5 + - + +
137N TYR* 3.6 31.6 - - + -
157N HIS* 2.9 40.3 - - - +
160N SER* 4.9 3.2 + - - -
161N GLN* 3.5 26.3 + - + +
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Residues in contact with ASN 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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1372 TYR* 2.9 57.5 + - + +
1402 LYS* 1.3 88.3 - - - +
1422 PHE* 1.3 64.4 + - - +
1432 ARG* 3.6 16.9 + - - -
1462 MET* 4.6 3.3 - - - +
1542 PHE* 3.8 23.7 - - + -
137N TYR* 5.1 2.3 - - - -
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Residues in contact with PHE 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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62 VAL* 3.4 33.0 - - + -
72 THR* 4.1 6.7 - - - -
1232 PRO* 3.5 38.4 - - + -
1242 TYR* 3.5 33.0 - + + -
1382 CYS 2.8 22.5 + - - +
1392 ASP* 4.4 6.6 + - - +
1402 LYS 3.8 1.6 - - - +
1412 ASN* 1.3 74.3 - - - +
1432 ARG* 1.3 85.5 + - - +
1442 GLU* 4.0 20.9 - - + -
1462 MET* 4.8 2.0 - - - -
1542 PHE* 3.7 14.3 - + + -
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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