Contacts of the helix formed by residues 139 - 158 (chain 7) in PDB entry 5U8T
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 LEU 139 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2644 TYR* 3.4 7.5 + - - -
3204 ASN 5.9 3.8 - - - +
3224 ILE* 5.8 6.3 - - + -
1377 ASP 3.7 0.6 + - - -
1387 VAL* 1.3 82.2 - - + +
1407 ASP* 1.3 59.2 + - - +
1417 VAL* 4.3 0.4 - - - +
1427 ILE* 3.2 32.3 - - + -
1437 LEU* 2.8 41.1 + - + +
3037 ARG* 3.2 30.7 - - + +
3047 ALA 5.7 0.2 - - - -
3057 SER 4.3 11.7 - - - +
3067 LYS* 5.9 10.3 - - + +
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Residues in contact with ASP 140 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737 ARG* 4.3 15.1 - - - -
1327 ILE* 4.1 15.8 - - - +
1337 ASP 5.1 0.6 - - - +
1347 TYR* 3.3 23.9 - - - +
1377 ASP* 3.3 29.8 + - + +
1387 VAL 3.0 4.9 + - - -
1397 LEU* 1.3 78.9 - - - +
1417 VAL* 1.3 58.7 + - - +
1437 LEU* 3.5 3.7 + - - +
1447 ASN* 2.9 32.6 + - - +
1997 ARG* 6.4 1.8 - - - -
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Residues in contact with VAL 141 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1824 GLY 3.4 9.6 - - - +
1844 ASN* 3.6 17.7 - - - +
2644 TYR* 3.2 26.9 - - - +
1347 TYR* 3.4 42.6 - - + -
1357 LYS* 3.4 24.7 - - + -
1377 ASP 4.1 2.7 - - - +
1397 LEU 4.3 0.7 - - - +
1407 ASP* 1.3 77.8 - - - +
1427 ILE* 1.3 61.0 + - - +
1447 ASN* 3.8 7.6 - - + -
1457 GLN* 2.9 39.4 + - + +
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Residues in contact with ILE 142 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1814 TRP* 5.2 1.8 - - + +
1824 GLY* 3.9 29.9 - - - +
2644 TYR* 4.1 14.1 - - + +
1397 LEU* 2.9 35.8 + - + +
1417 VAL* 1.3 79.9 - - - +
1437 LEU* 1.3 52.0 + - + +
1457 GLN* 3.4 2.1 + - - +
1467 ARG* 2.7 71.6 + - + +
3037 ARG* 3.9 42.4 - - + +
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Residues in contact with LEU 143 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1397 LEU* 2.8 28.3 + - + +
1407 ASP* 4.2 4.0 - - - +
1427 ILE* 1.3 70.9 - - + +
1447 ASN* 1.3 66.4 + - - +
1467 ARG* 3.0 22.0 - - + +
1477 ARG* 2.9 39.9 + - + +
1927 PHE* 4.8 2.2 - - + -
1967 LEU* 3.7 28.0 - - + +
1977 THR* 3.5 30.5 - - + -
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Residues in contact with ASN 144 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1327 ILE* 4.8 10.3 - - - +
1337 ASP 4.6 6.1 + - - -
1347 TYR* 4.3 19.7 - - + +
1407 ASP* 2.9 22.4 + - - +
1417 VAL* 3.8 9.0 - - + +
1437 LEU* 1.3 77.8 - - - +
1457 GLN* 1.3 61.0 + - + +
1477 ARG* 3.7 2.4 + - - +
1487 LEU* 2.9 35.7 + - - +
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Residues in contact with GLN 145 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1794 ILE* 5.4 3.9 - - - +
1814 TRP 3.2 22.2 - - - +
1824 GLY* 3.2 8.4 - - - -
1844 ASN* 2.9 39.3 + - - +
1347 TYR* 5.7 3.0 - - - -
1417 VAL* 2.9 23.8 + - + +
1427 ILE 3.5 2.2 - - - +
1447 ASN* 1.3 76.3 - - + +
1467 ARG* 1.3 59.4 + - - +
1487 LEU* 4.0 11.4 - - + -
1497 ARG* 2.9 37.3 + - + +
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Residues in contact with ARG 146 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1814 TRP* 3.8 38.2 - - - +
1427 ILE* 2.7 41.0 + - - +
1437 LEU* 3.0 31.6 + - + +
1457 GLN* 1.3 78.4 - - - +
1477 ARG* 1.3 60.4 + - - +
1497 ARG* 3.3 10.8 - - - +
1507 ASN* 2.8 29.7 + - - +
1927 PHE* 4.1 14.6 - - + -
1967 LEU* 6.3 1.0 - - - +
2597 ALA* 4.7 5.4 - - - +
2687 GLU* 6.2 4.7 - - - -
2707 PHE* 5.8 3.7 - - - -
3017 SER* 5.4 0.2 - - - -
3037 ARG* 3.5 5.5 + - - +
3047 ALA* 3.2 51.9 + - - +
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Residues in contact with ARG 147 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437 LEU* 2.9 17.8 + - + +
1447 ASN 4.4 1.6 - - - +
1467 ARG* 1.3 79.2 - - - +
1487 LEU* 1.3 59.6 + - - +
1507 ASN* 3.6 11.8 + - - +
1517 GLU* 3.0 30.8 + - - +
1917 LEU* 3.2 31.4 - - - +
1927 PHE* 3.1 53.9 + - + +
1937 PRO 4.1 4.8 + - - -
1947 PRO* 5.5 0.8 - - - +
1967 LEU* 4.1 1.4 - - - +
1977 THR* 3.1 38.4 + - - +
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Residues in contact with LEU 148 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1447 ASN* 2.9 29.7 + - - +
1457 GLN* 4.0 10.1 - - + -
1477 ARG* 1.3 77.2 - - - +
1497 ARG* 1.3 60.9 + - - +
1507 ASN 3.1 0.2 - - - -
1517 GLU* 4.3 5.0 - - - +
1527 ARG* 2.9 50.6 + - + +
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Residues in contact with ARG 149 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1814 TRP* 3.2 50.3 - - - -
1457 GLN* 2.9 27.8 + - + +
1467 ARG* 3.3 13.8 - - - +
1487 LEU* 1.3 77.7 - - - +
1507 ASN* 1.3 60.0 + - - +
1527 ARG* 4.2 6.5 - - - +
1537 MET* 2.9 57.1 + - + +
2677 TYR* 5.3 6.9 + - - +
2687 GLU* 4.8 13.5 + - - +
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Residues in contact with ASN 150 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467 ARG 2.8 18.6 + - - +
1477 ARG* 3.6 13.4 + - - +
1487 LEU 3.1 0.2 - - - -
1497 ARG* 1.3 79.5 - - + +
1517 GLU* 1.3 57.0 + - - +
1537 MET* 3.6 3.0 - - - +
1547 LEU* 2.7 48.9 + - - +
1917 LEU* 5.0 11.1 - - - +
1927 PHE* 3.2 43.8 - - + -
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Residues in contact with GLU 151 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477 ARG 3.0 19.1 + - - +
1487 LEU* 4.3 5.3 - - - +
1507 ASN* 1.3 78.2 - - - +
1527 ARG* 1.3 52.3 + - - +
1547 LEU* 3.2 15.7 - - + -
1557 SER* 2.4 48.0 + - - +
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Residues in contact with ARG 152 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1487 LEU* 2.9 37.0 + - + +
1497 ARG* 4.2 1.8 - - - +
1517 GLU* 1.3 76.7 - - - +
1537 MET* 1.3 89.9 + - + +
1547 LEU 3.2 0.2 - - - -
1557 SER* 3.5 9.9 - - - -
1567 ASP* 3.3 38.6 + - - +
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Residues in contact with MET 153 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1497 ARG* 2.9 45.1 + - + +
1507 ASN* 3.6 3.4 - - - +
1527 ARG* 1.3 118.6 - - + +
1547 LEU* 1.3 59.9 + - - +
1557 SER 3.3 0.2 - - - -
1567 ASP* 4.0 15.5 + - - +
1577 ARG* 3.9 20.4 + - - +
2677 TYR* 5.8 6.9 - - + -
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Residues in contact with LEU 154 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1507 ASN* 2.7 33.2 + - - +
1517 GLU* 3.2 15.9 - - + +
1527 ARG 3.2 0.2 - - - -
1537 MET* 1.3 77.4 - - - +
1557 SER* 1.3 59.2 + - - +
1567 ASP 3.4 0.9 - - - -
1577 ARG* 3.3 34.8 + - - +
1587 THR* 3.2 36.4 + - + +
1907 GLU 5.2 9.0 - - - +
1917 LEU* 6.1 5.2 - - + -
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Residues in contact with SER 155 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517 GLU* 2.4 43.0 + - - +
1527 ARG* 3.3 15.2 + - - -
1547 LEU* 1.3 76.7 - - - +
1567 ASP* 1.3 63.7 + - - +
1587 THR* 3.5 9.3 - - - +
1597 ASN* 3.1 28.8 + - - +
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Residues in contact with ASP 156 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1527 ARG* 3.3 25.0 + - - +
1537 MET* 4.0 22.6 + - - +
1547 LEU 3.4 0.2 - - - -
1557 SER* 1.3 81.8 - - - +
1577 ARG* 1.3 62.2 + - - +
1597 ASN* 3.5 22.0 + - - +
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Residues in contact with ARG 157 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1537 MET 3.9 13.1 + - - +
1547 LEU* 3.3 44.3 + - - +
1557 SER 3.4 0.4 - - - -
1567 ASP* 1.3 81.3 - - - +
1587 THR* 1.3 57.0 + - - +
1597 ASN 3.3 3.4 + - - -
2677 TYR* 4.0 31.5 - - - -
2877 GLU* 4.9 14.4 + - - -
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Residues in contact with THR 158 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1547 LEU* 3.2 28.6 + - + +
1557 SER* 3.5 14.1 - - - +
1577 ARG* 1.3 77.9 - - - +
1597 ASN* 1.3 62.1 + - + +
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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