Contacts of the helix formed by residues 149 - 163 (chain 2) in PDB entry 3EXG
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 ASN 149 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52 VAL* 3.8 6.1 - - - -
1482 TRP* 1.3 110.2 - - + +
1502 SER* 1.3 59.6 + - - +
1512 GLU* 3.5 12.2 + - - +
1522 ASP* 3.1 23.5 + - - +
1532 ALA* 2.9 26.5 + - - +
1802 PHE* 3.3 39.0 - - + +
1992 LYS* 6.2 0.8 - - - +
2012 GLU* 4.4 5.3 + - - -
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Residues in contact with SER 150 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32 VAL* 2.8 27.2 + - - -
42 THR 3.1 15.6 - - - -
52 VAL* 3.2 8.3 + - - +
82 ALA* 3.3 24.3 - - - +
1492 ASN* 1.3 73.8 - - - +
1512 GLU* 1.3 66.7 + - - +
1532 ALA* 3.1 2.2 + - - -
1542 LYS* 2.9 22.2 + - - +
1802 PHE* 3.6 16.7 - - - -
1822 PHE* 3.8 15.5 - - - -
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Residues in contact with GLU 151 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1492 ASN* 3.5 15.0 - - - +
1502 SER* 1.3 78.6 - - - +
1522 ASP* 1.3 65.4 + - - +
1542 LYS* 4.3 0.2 - - - -
1552 GLY 3.3 6.2 + - - -
1802 PHE* 5.5 0.8 - - + +
1812 GLU 4.2 6.3 - - - +
1822 PHE* 4.1 11.4 - - + -
1832 PRO* 3.0 38.4 - - - +
1852 GLU* 4.9 4.7 - - - +
1862 ALA* 4.8 3.4 - - + -
1912 PHE* 3.2 43.1 - - + -
1932 ILE* 3.7 3.3 - - + +
1992 LYS* 4.7 15.7 + - - -
2392 ARG* 5.6 1.7 + - - +
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Residues in contact with ASP 152 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472 PRO* 4.1 5.1 - - + +
1482 TRP* 3.0 21.8 + - - +
1492 ASN* 3.1 17.9 + - - +
1512 GLU* 1.3 73.2 - - - +
1532 ALA* 1.3 61.2 + - - +
1542 LYS 3.1 2.2 - - - -
1562 LEU* 2.8 53.0 + - + +
1932 ILE* 3.6 10.1 - - + -
1992 LYS* 4.7 4.3 - - - +
2012 GLU* 4.7 1.0 - - - +
2372 ASN* 3.3 18.2 + - - +
2392 ARG* 3.3 32.3 + - - +
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Residues in contact with ALA 153 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52 VAL* 3.6 27.4 - - + -
82 ALA* 4.5 2.0 - - + -
92 ILE* 3.8 19.8 - - + +
1472 PRO* 3.6 20.7 - - + +
1492 ASN 2.9 17.5 + - - +
1502 SER* 3.1 5.8 + - - +
1522 ASP* 1.3 78.0 - - - +
1542 LYS* 1.3 63.1 - - - +
1562 LEU* 4.4 0.3 - - - +
1572 ILE* 3.2 23.9 + - - +
1692 VAL* 6.0 0.9 - - - +
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Residues in contact with LYS 154 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82 ALA* 3.5 26.4 - - + +
112 GLN* 2.5 34.7 + - - +
122 GLY 3.9 7.0 - - - +
152 GLU* 3.0 36.2 + - - -
1502 SER 2.9 13.6 + - - +
1512 GLU 4.3 2.5 - - - +
1532 ALA* 1.3 78.9 - - - +
1552 GLY* 1.3 60.6 - - - +
1572 ILE* 2.8 25.5 - - - +
1582 LYS* 3.2 17.0 + - + +
1822 PHE* 4.0 10.5 - - + -
1862 ALA 3.2 27.0 + - - +
1872 GLN 3.6 2.8 + - - -
1882 SER 3.4 7.7 + - - -
1912 PHE* 4.1 7.4 - - + -
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Residues in contact with GLY 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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1512 GLU 3.3 10.0 + - - -
1542 LYS* 1.3 78.1 - - - +
1562 LEU* 1.3 56.1 + - - +
1582 LYS 4.0 1.1 - - - -
1592 SER* 2.9 31.4 + - - -
1912 PHE* 3.9 18.6 - - - -
1922 LEU* 3.8 1.2 - - - -
1932 ILE* 3.0 32.8 + - - -
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Residues in contact with LEU 156 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1452 VAL* 4.2 29.3 - - + +
1472 PRO* 3.9 22.7 - - + -
1522 ASP* 2.8 41.5 + - + +
1532 ALA 4.4 1.3 - - - +
1552 GLY* 1.3 70.7 - - - +
1572 ILE* 1.3 61.0 + - - +
1592 SER* 3.3 1.5 + - - -
1602 ALA* 2.7 33.4 + - - +
1692 VAL* 5.0 3.8 - - + +
1932 ILE* 3.8 30.5 - - + +
1942 PRO 5.0 0.7 - - - +
1952 ILE* 4.7 11.7 - - + +
2392 ARG* 4.0 28.3 - - + +
2402 THR* 5.1 0.7 - - - +
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Residues in contact with ILE 157 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92 ILE* 4.5 14.8 - - + +
122 GLY* 4.3 10.3 - - - -
132 MET* 4.2 20.9 - - + +
772 ILE* 5.3 1.1 - - + -
1132 VAL* 4.2 21.1 - - + -
1152 ARG* 4.2 22.9 - - + -
1532 ALA 3.2 15.7 + - - +
1542 LYS* 2.8 27.8 - - - +
1562 LEU* 1.3 79.6 - - - +
1582 LYS* 1.3 63.0 + - + +
1602 ALA* 3.3 1.5 + - - -
1612 ILE* 2.8 45.4 + - + +
1692 VAL* 4.5 16.7 - - + +
1712 GLU* 5.3 1.3 - - - +
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Residues in contact with LYS 158 (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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122 GLY* 3.7 17.0 - - - -
152 GLU* 2.8 38.3 + - - +
162 GLU* 3.1 35.4 + - + +
1542 LYS* 3.2 29.6 + - + +
1552 GLY 4.2 0.7 - - - +
1572 ILE* 1.3 80.1 - - + +
1592 SER* 1.3 60.7 + - - +
1612 ILE* 3.8 1.6 - - - +
1622 ARG* 2.8 35.0 + - - +
1892 LYS 2.9 22.6 + - - -
1912 PHE 3.1 27.4 - - - +
1922 LEU* 3.6 17.0 - - + -
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Residues in contact with SER 159 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1552 GLY 2.9 18.9 + - - -
1562 LEU 3.8 3.1 - - - -
1582 LYS* 1.3 75.2 - - - +
1602 ALA* 1.3 57.9 - - - +
1622 ARG* 3.3 6.6 + - - +
1632 ASP* 2.8 30.1 + - - +
1922 LEU* 3.6 13.3 - - - +
1932 ILE 2.9 31.4 + - - -
1942 PRO* 4.6 1.2 - - - +
1952 ILE* 4.1 16.9 - - - +
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Residues in contact with ALA 160 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132 VAL* 3.4 12.6 - - + +
1452 VAL* 5.6 0.7 - - + -
1562 LEU 2.7 21.5 + - - +
1572 ILE 3.7 3.6 - - - +
1592 SER* 1.3 70.5 - - - +
1612 ILE* 1.3 67.1 + - - +
1632 ASP* 3.1 11.5 + - - +
1672 VAL* 3.4 34.5 - - + +
1692 VAL* 3.9 14.4 - - + -
1952 ILE* 4.1 10.7 - - + +
10152 K 3.1 12.0 - - - -
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Residues in contact with ILE 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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132 MET* 4.7 7.6 - - - +
162 GLU* 3.6 41.1 - - + +
192 ARG* 5.9 0.9 - - - +
232 VAL* 4.2 23.6 - - + -
752 ARG* 3.3 10.9 + - + +
772 ILE* 3.4 38.4 - - + -
1132 VAL* 3.7 8.1 - - + -
1572 ILE* 2.8 37.3 + - + +
1582 LYS 3.8 3.6 - - - +
1602 ALA* 1.3 71.4 - - - +
1622 ARG* 1.3 61.7 + - - +
10152 K 2.5 23.3 - - - -
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Residues in contact with ARG 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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162 GLU* 2.4 44.3 + - - -
192 ARG* 3.3 52.8 - - - +
752 ARG* 2.9 15.9 + - - +
1582 LYS* 2.8 27.4 + - - +
1592 SER* 3.7 6.3 - - - +
1612 ILE* 1.3 77.2 - - - +
1632 ASP* 1.3 61.5 + - - +
1642 ASN* 3.7 5.9 + - - -
1892 LYS 4.6 2.0 + - - -
1902 ASP* 4.7 17.8 + - - +
1922 LEU* 3.7 33.8 - - + +
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Residues in contact with ASP 163 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3431 ASP* 3.9 7.3 - - - +
752 ARG* 3.4 2.3 + - - -
1432 LYS* 3.1 35.4 + - - +
1592 SER 2.8 19.3 + - - +
1602 ALA* 3.1 9.4 + - - +
1622 ARG* 1.3 76.1 - - - +
1642 ASN* 1.3 60.7 + - - +
1652 ASN* 2.8 43.9 + - - +
1672 VAL* 4.0 10.1 - - + +
1952 ILE* 4.7 5.4 - - + +
10152 K 2.6 27.4 - - - -
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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
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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