Contacts of the helix formed by residues 147 - 166 (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 SER 147 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82 PHE* 3.8 2.9 - - - -
92 LYS* 4.9 9.9 - - - -
102 ASP* 5.5 0.9 - - - -
1462 MET* 1.3 73.7 - - - +
1482 LYS* 1.3 66.8 + - - +
1492 GLU* 3.1 21.5 + - - -
1502 GLU* 2.7 37.4 + - - +
1512 THR* 2.9 23.7 + - - -
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Residues in contact with LYS 148 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82 PHE* 3.6 32.1 - - + -
102 ASP* 4.7 8.2 + - - +
132 ILE* 4.1 4.2 - - + +
1472 SER* 1.3 74.2 - - - +
1492 GLU* 1.3 61.7 + - + +
1512 THR* 3.8 2.2 - - - -
1522 VAL* 3.0 46.0 + - + +
1772 VAL* 4.4 16.2 - - + -
1792 THR* 6.1 1.3 - - + -
1852 GLU* 2.6 38.7 + - - -
1872 LEU* 5.2 3.6 - - - -
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Residues in contact with GLU 149 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472 SER* 3.1 21.3 + - - +
1482 LYS* 1.3 80.1 + - + +
1502 GLU* 1.3 65.0 + - + +
1522 VAL* 3.4 6.5 + - - +
1532 ASP* 3.1 31.6 + - - +
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Residues in contact with GLU 150 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1432 ARG* 3.1 30.6 + - - +
1452 ASN 4.7 0.3 - - - +
1462 MET* 3.2 30.5 - - + +
1472 SER* 2.7 39.2 + - - +
1492 GLU* 1.3 76.8 - - + +
1512 THR* 1.3 58.1 + - - +
1532 ASP* 3.0 10.2 + - - +
1542 PHE 2.8 25.1 + - - -
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Residues in contact with THR 151 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62 VAL* 4.0 29.2 - - + +
82 PHE* 3.0 31.9 - - + +
132 ILE* 3.5 30.1 - - + -
1462 MET* 3.5 15.7 - - - +
1472 SER 2.9 11.7 + - - -
1482 LYS 3.8 4.0 - - - -
1502 GLU* 1.3 71.6 - - - +
1522 VAL* 1.3 65.4 + - - +
1532 ASP 2.9 1.7 + - - -
1542 PHE* 3.0 3.6 + - + +
1552 ILE* 2.9 26.1 + - + +
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Residues in contact with VAL 152 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132 ILE* 3.7 18.6 - - + -
182 PHE* 3.7 30.1 - - - -
1482 LYS* 3.0 32.4 + - + +
1492 GLU* 3.8 6.5 - - - +
1502 GLU 3.4 0.2 - - - -
1512 THR* 1.3 75.2 - - - +
1532 ASP* 1.3 62.7 + - - +
1552 ILE* 4.7 0.4 - - - -
1562 LYS* 3.0 29.0 + - - +
1752 MET* 3.4 15.9 - - - +
1872 LEU* 3.9 19.7 - - + -
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Residues in contact with ASP 153 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1492 GLU* 3.1 18.7 + - - +
1502 GLU* 3.0 12.7 + - - +
1512 THR 2.9 0.6 - - - -
1522 VAL* 1.3 82.2 - - - +
1542 PHE* 1.3 61.6 + - - +
1552 ILE 3.2 0.4 - - - -
1562 LYS* 3.8 19.5 + - - +
1572 HIS* 2.9 49.8 + - + +
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Residues in contact with PHE 154 (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* 3.6 17.3 - - + -
62 VAL* 3.8 30.1 - - + -
1242 TYR* 4.2 4.7 - + - -
1372 TYR* 4.5 4.0 - + - -
1382 CYS* 3.8 36.8 - - + -
1412 ASN* 3.8 22.7 - - + -
1422 PHE* 3.7 39.3 - + + -
1462 MET* 3.8 16.4 - - + -
1502 GLU 2.8 12.7 + - - +
1512 THR* 3.5 6.7 - - - +
1532 ASP* 1.3 75.1 - - - +
1552 ILE* 1.3 57.4 + - + +
1572 HIS* 4.0 3.7 - - - +
1582 SER* 2.8 43.2 + - - -
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Residues in contact with ILE 155 (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* 4.0 14.4 - - + -
62 VAL* 3.5 33.2 - - + +
132 ILE* 3.7 42.6 - - + +
152 GLY* 4.2 9.6 - - - +
1512 THR* 2.9 18.2 + - + +
1542 PHE* 1.3 74.7 - - + +
1562 LYS* 1.3 65.8 + - - +
1592 LEU* 3.0 44.1 + - + +
1752 MET* 3.5 26.9 - - + -
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Residues in contact with LYS 156 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 LEU* 2.7 103.6 - - + +
1522 VAL* 3.0 21.8 + - - +
1532 ASP* 3.3 23.1 + - - +
1552 ILE* 1.3 75.9 - - - +
1572 HIS* 1.3 63.5 + - - +
1602 SER* 3.1 24.1 + - - -
1732 ILE* 3.8 10.7 - - + +
1752 MET* 3.9 10.3 - - + -
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Residues in contact with HIS 157 (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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182 LEU* 4.0 33.0 + - - +
1372 TYR* 3.3 24.2 - - + +
1532 ASP* 2.9 41.6 + - + +
1542 PHE* 4.0 2.5 - - - +
1562 LYS* 1.3 78.4 - - + +
1582 SER* 1.3 66.2 + - - +
1602 SER* 2.7 21.1 + - - -
1612 GLN* 3.1 13.5 + - - +
140N LYS* 2.9 34.4 + - - +
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Residues in contact with SER 158 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42 MET* 3.6 21.6 - - - +
1342 ILE* 3.2 17.2 - - - +
1372 TYR* 3.5 20.0 - - - -
1382 CYS* 3.3 27.5 - - - -
1542 PHE* 2.8 27.7 + - - -
1572 HIS* 1.3 75.8 - - - +
1592 LEU* 1.3 58.7 + - - +
1612 GLN* 3.0 5.5 + - - +
1622 ALA* 2.9 22.5 + - - +
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Residues in contact with LEU 159 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22 SER* 4.1 29.2 - - - +
32 ILE 4.4 2.7 - - - +
42 MET* 3.8 23.8 - - + -
152 GLY* 3.6 10.5 - - - -
162 ALA* 3.4 36.6 - - - +
172 ASP* 5.9 0.4 - - + +
1342 ILE* 4.5 8.7 - - + -
1552 ILE* 3.0 21.7 + - + +
1582 SER* 1.3 75.2 - - - +
1602 SER* 1.3 60.9 + - - +
1622 ALA* 3.5 2.3 - - - +
1632 ILE* 2.9 36.2 + - + +
1732 ILE* 3.9 29.6 - - + -
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Residues in contact with SER 160 (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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182 TYR* 3.6 55.5 + - - +
1562 LYS 3.1 16.5 + - - -
1572 HIS* 2.7 23.5 + - - -
1592 LEU* 1.3 77.3 - - - +
1612 GLN* 1.3 61.0 + - - +
1632 ILE* 3.7 3.6 - - - +
1642 LYS* 2.9 27.0 + - - +
1732 ILE* 4.0 2.0 - - - +
140N LYS* 4.8 2.6 + - - -
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Residues in contact with GLN 161 (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* 3.6 13.7 - - + -
1372 TYR* 5.3 3.6 - - + -
1572 HIS 3.1 9.8 + - - +
1582 SER* 3.0 10.8 + - - +
1602 SER* 1.3 83.2 + - - +
1622 ALA* 1.3 67.2 + - - +
1642 LYS* 3.0 18.0 + - - +
1652 TRP* 2.9 43.8 + - - +
136N GLY* 2.9 34.3 + - - -
139N ASP* 2.8 23.7 - - - +
140N LYS* 3.5 29.0 + - + +
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Residues in contact with ALA 162 (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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22 SER* 3.4 28.0 - - - +
1302 GLY 3.5 21.8 - - - +
1332 PHE* 4.4 3.5 - - - -
1342 ILE* 3.6 16.0 - - + +
1582 SER 2.9 12.2 + - - +
1592 LEU* 3.5 9.4 - - - +
1612 GLN* 1.3 76.3 - - - +
1632 ILE* 1.3 57.9 + - - +
1652 TRP* 3.3 1.2 + - - +
1662 ASP* 2.9 33.1 + - - +
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Residues in contact with ILE 163 (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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22 SER* 5.0 2.5 - - - +
172 ASP* 4.0 19.5 - - + -
182 TYR* 3.7 33.4 - - + -
1592 LEU* 2.9 21.6 + - + +
1602 SER* 3.7 3.8 - - - +
1622 ALA* 1.3 77.4 - - - +
1642 LYS* 1.3 64.3 - - - +
1662 ASP 3.4 14.4 - - - +
1692 SER* 4.0 15.8 - - - +
1702 GLY* 3.7 32.3 - - - +
1712 GLY 4.8 0.7 - - - +
1722 VAL 4.9 0.2 - - - +
1732 ILE* 3.8 23.8 - - + -
26M LEU* 4.2 5.2 - - - +
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Residues in contact with LYS 164 (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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182 GLU 5.8 1.6 - - - -
1602 SER 2.9 15.2 + - - +
1612 GLN* 3.0 21.0 + - - +
1632 ILE* 1.3 79.1 - - - +
1652 TRP* 1.3 81.3 + - + +
26M LEU* 3.4 23.0 - - - +
29M ASN* 5.7 5.8 - - - +
139N ASP* 2.7 39.6 + - - +
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Residues in contact with TRP 165 (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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1332 PHE* 3.8 25.7 - - + -
1612 GLN* 2.9 49.3 + - - +
1642 LYS* 1.3 95.9 - - + +
1662 ASP* 1.3 59.7 + - - +
25M LEU* 3.5 15.4 - - + +
26M LEU* 2.9 54.1 + - - -
27M ARG 3.7 15.0 - - - -
29M ASN* 4.8 6.7 - - - -
124N TYR* 5.7 2.2 - - - -
135N TYR* 3.6 49.6 + + + -
136N GLY 4.2 2.0 - - - -
139N ASP* 3.8 29.4 - - + -
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Residues in contact with ASP 166 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1292 SER* 2.7 30.0 + - - -
1302 GLY* 3.1 18.5 + - - -
1332 PHE* 3.6 12.3 - - + -
1622 ALA 2.9 16.9 + - - +
1632 ILE 3.4 9.5 - - - +
1652 TRP* 1.3 77.8 - - - +
1672 GLY* 1.3 58.4 + - - +
1682 SER* 3.2 17.5 + - - -
1692 SER* 2.7 48.9 + - - +
24M SER* 4.0 11.1 + - - +
26M LEU* 4.3 1.1 - - - +
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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
------------------------------------------------------------
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