Contacts of the helix formed by residues 140 - 156 (chain 1) 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 ALA 140 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1351 ASN* 5.5 4.7 - - + -
1371 ILE* 3.3 34.3 + - + +
1381 VAL 3.3 0.2 - - - -
1391 GLY* 1.3 76.2 - - - +
1411 GLN* 1.3 62.0 + - - +
1421 VAL 3.1 1.0 + - - -
1431 PRO* 3.4 3.5 - - - +
1441 LEU* 3.4 12.5 - - + +
1741 GLN* 3.2 11.5 - - - +
912 ASP* 4.0 9.0 - - - +
922 GLN* 3.1 33.2 + - - +
952 ASN* 6.5 0.2 - - + -
962 SER* 4.3 6.7 - - - +
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Residues in contact with GLN 141 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861 ILE* 3.9 8.3 - - + +
871 THR* 3.4 28.5 - - - +
881 ALA* 3.2 31.1 - - - +
1351 ASN* 3.6 17.1 - - + +
1371 ILE 4.2 3.4 + - - +
1391 GLY* 2.9 22.6 + - - +
1401 ALA* 1.3 71.5 + - - +
1421 VAL* 1.3 63.9 + - + +
1431 PRO 3.6 0.2 - - - -
1441 LEU* 3.6 12.9 - - - +
1451 GLY* 2.8 23.0 + - - -
1631 THR* 3.5 7.1 - - + +
1641 LEU 3.2 20.8 + - - +
1651 TYR* 3.5 14.3 - - - +
1691 ALA* 5.5 0.8 - - - +
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Residues in contact with VAL 142 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391 GLY* 2.9 13.6 + - - +
1411 GLN* 1.3 92.2 - - - +
1431 PRO* 1.3 65.8 - - + +
1451 GLY* 3.2 1.6 + - - -
1461 ALA* 3.0 25.6 + - - +
1631 THR* 3.5 10.0 - - + +
1651 TYR* 3.9 22.0 - - + -
1751 ILE* 3.5 35.9 - - + -
1781 ALA* 4.2 8.5 - - + -
1911 PHE* 3.6 31.1 - - + -
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Residues in contact with PRO 143 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391 GLY 3.2 14.4 - - - +
1401 ALA 3.4 6.5 - - - +
1421 VAL* 1.3 90.7 - - + +
1441 LEU* 1.3 59.8 + - - +
1461 ALA* 3.3 6.5 + - + +
1471 GLY 2.9 22.2 + - - -
1741 GLN* 3.4 41.1 - - + +
1781 ALA* 4.4 5.2 - - + -
612 GLY* 3.6 25.6 - - - +
642 GLY* 3.4 20.9 - - - +
652 ILE* 3.4 7.3 - - + +
922 GLN* 3.9 1.6 - - - +
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Residues in contact with LEU 144 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861 ILE* 3.6 17.0 - - + -
1351 ASN* 4.0 20.2 - - - +
1401 ALA* 3.4 19.4 + - + +
1411 GLN* 3.4 7.4 + - - +
1421 VAL 3.3 0.4 - - - -
1431 PRO* 1.3 74.2 - - - +
1451 GLY* 1.3 61.7 + - - +
1471 GLY* 3.1 1.7 + - - -
1481 ILE* 2.8 35.5 + - + +
642 GLY 3.4 18.4 - - - +
672 VAL* 3.5 21.8 - - + -
682 GLY* 3.4 18.5 - - - +
712 MET* 4.2 10.5 - - - -
922 GLN* 4.2 4.5 - - - +
962 SER* 3.5 25.8 - - - +
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Residues in contact with GLY 145 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861 ILE* 3.8 13.0 - - - +
1411 GLN 2.8 16.5 + - - -
1421 VAL 3.2 1.1 + - - -
1431 PRO 3.2 0.2 - - - -
1441 LEU* 1.3 76.5 - - - +
1461 ALA* 1.3 63.9 + - - +
1481 ILE* 3.3 1.7 + - - -
1491 ALA* 3.1 20.4 + - - +
1611 CYS* 3.6 12.6 - - - -
1631 THR* 3.2 24.0 + - - -
1891 CYS* 4.1 0.6 - - - -
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Residues in contact with ALA 146 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1421 VAL 3.0 14.5 + - - +
1431 PRO 3.8 7.0 - - - +
1441 LEU 3.2 0.4 - - - -
1451 GLY* 1.3 76.1 - - - +
1471 GLY* 1.3 50.6 + - - +
1491 ALA* 3.3 5.4 + - - +
1501 LEU* 2.8 32.8 + - - +
1631 THR* 4.1 0.6 + - - -
1781 ALA* 4.3 17.7 - - + +
1821 ALA* 5.1 0.7 - - + -
1871 LEU* 3.7 13.4 - - + +
1891 CYS* 3.9 12.1 - - - -
1911 PHE* 4.4 10.1 - - + -
652 ILE* 4.0 19.5 - - + -
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Residues in contact with GLY 147 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431 PRO 2.9 12.8 + - - -
1441 LEU 3.4 4.3 - - - -
1451 GLY 3.1 0.2 - - - -
1461 ALA* 1.3 73.7 - - - +
1481 ILE* 1.3 64.0 - - - +
1501 LEU* 3.0 6.5 + - - +
1511 ALA 3.0 17.3 + - - -
652 ILE* 3.5 33.6 - - - +
682 GLY* 3.9 0.7 - - - -
692 ALA* 3.8 14.5 + - - -
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Residues in contact with ILE 148 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841 HIS* 3.4 43.5 - - + +
861 ILE* 4.0 18.8 - - + -
1321 TYR* 3.3 41.7 - - + +
1441 LEU* 2.8 25.8 + - + +
1451 GLY* 3.3 4.7 + - - +
1471 GLY* 1.3 71.0 - - - +
1491 ALA* 1.3 62.6 + - - +
1511 ALA* 3.1 5.9 + - - +
1521 CYS* 3.0 20.3 + - - -
1611 CYS* 3.6 10.1 - - + -
682 GLY* 3.6 17.2 - - - +
712 MET* 5.0 2.0 - - + -
722 ALA* 3.9 16.8 - - + -
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Residues in contact with ALA 149 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1451 GLY 3.1 10.0 + - - +
1461 ALA 3.4 8.3 - - - +
1481 ILE* 1.3 74.3 - - - +
1501 LEU* 1.3 66.8 + - - +
1521 CYS* 3.0 17.7 + - - +
1531 LYS 3.1 10.6 + - - -
1611 CYS* 3.8 10.5 - - + +
1871 LEU* 4.3 2.2 - - + -
1881 PRO* 3.4 35.6 - - + +
1891 CYS* 3.6 22.7 - - + -
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Residues in contact with LEU 150 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1461 ALA 2.8 14.4 + - - +
1471 GLY* 3.0 10.0 + - - +
1491 ALA* 1.3 76.3 - - - +
1511 ALA* 1.3 62.7 + - - +
1531 LYS* 3.4 7.8 + - + +
1541 TYR* 3.0 30.9 + - + +
1851 TRP* 4.8 13.9 - - + -
1871 LEU* 3.8 28.6 - - + +
242 PHE* 4.0 31.6 - - + -
262 LEU* 5.8 0.7 - - + -
532 ILE* 4.6 14.1 - - + -
652 ILE* 4.2 20.9 - - + -
692 ALA* 4.3 8.5 - - + -
742 LEU* 5.7 0.4 - - + -
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Residues in contact with ALA 151 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471 GLY 3.0 10.0 + - - +
1481 ILE 3.3 9.9 - - - +
1491 ALA 3.1 0.2 - - - -
1501 LEU* 1.3 75.9 - - - +
1521 CYS* 1.3 67.1 + - - +
1541 TYR* 3.1 2.8 + - - +
1551 ASN* 3.0 32.0 + - - +
692 ALA* 4.4 4.0 - - - +
722 ALA* 3.7 26.2 - - + +
742 LEU* 3.7 28.0 - - + -
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Residues in contact with CYS 152 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841 HIS* 4.0 18.8 - - - -
1481 ILE* 3.0 19.1 + - - -
1491 ALA* 3.0 11.0 + - - +
1511 ALA* 1.3 74.3 - - - +
1531 LYS* 1.3 65.1 + - - +
1541 TYR 2.9 1.0 + - - -
1551 ASN* 2.9 13.5 + - - +
1561 GLY* 3.0 10.6 + - - -
1571 LYS 4.2 3.5 + - - -
1581 ASP 5.2 0.4 + - - -
1591 GLU* 3.3 57.0 - - + +
1601 VAL* 4.1 10.3 - - - -
1611 CYS* 4.9 0.2 - - - -
1881 PRO* 3.8 5.8 - - + -
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Residues in contact with LYS 153 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491 ALA 3.1 4.0 + - - +
1501 LEU* 3.8 11.2 - - + +
1521 CYS* 1.3 78.9 - - - +
1541 TYR* 1.3 62.9 + - - +
1561 GLY* 3.3 12.6 + - - +
1851 TRP* 3.1 37.8 + - - +
1861 LYS* 4.1 9.2 - - - +
1871 LEU* 4.6 7.4 - - + -
1881 PRO* 4.1 18.9 - - + +
502 LYS* 5.2 1.6 - - - -
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Residues in contact with TYR 154 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1501 LEU* 3.0 26.7 + - + +
1511 ALA 3.3 5.6 - - - +
1521 CYS 2.9 0.6 + - - -
1531 LYS* 1.3 80.9 - - - +
1551 ASN* 1.3 64.4 + - - +
1561 GLY 3.3 0.2 - - - -
212 GLU* 2.6 30.8 + - + -
222 LYS* 4.1 4.1 - - + -
232 VAL 3.8 4.7 + - - -
242 PHE* 4.0 21.0 - + + +
502 LYS* 3.3 65.8 + - + +
512 ARG* 2.8 24.7 + - - -
532 ILE* 6.0 0.9 - - + -
742 LEU* 3.6 31.4 - - + -
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Residues in contact with ASN 155 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1511 ALA* 3.0 22.8 + - - +
1521 CYS 2.9 5.1 + - - +
1541 TYR* 1.3 81.3 - - - +
1561 GLY* 1.3 66.9 + - - +
1571 LYS* 3.5 28.1 - - + +
1591 GLU* 4.7 9.6 + - - +
222 LYS* 5.2 6.2 - - - +
722 ALA 5.1 5.3 + - - -
742 LEU* 3.9 24.9 - - - +
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Residues in contact with GLY 156 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521 CYS 3.0 7.4 + - - -
1531 LYS* 3.3 13.2 + - - -
1541 TYR 3.3 0.6 - - - -
1551 ASN* 1.3 81.1 - - - +
1571 LYS* 1.3 65.9 + - - +
1581 ASP 3.6 2.2 - - - -
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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
------------------------------------------------------------
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