Contacts of the helix formed by residues 139 - 155 (chain 1) in PDB entry 6Q8W
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 ARG 139 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361 GLY 6.1 0.2 - - - +
1371 GLU 3.8 4.0 + - - -
1381 TYR* 1.3 74.8 - - - +
1401 ARG* 1.3 63.4 + - - +
1421 ALA* 3.2 3.8 + - - +
1431 ASP* 2.6 62.6 + - - +
1751 ARG* 4.1 25.4 - - - +
362 GLN* 5.6 2.0 + - - -
1352 GLN* 5.6 0.9 - - - +
1382 ASP* 3.1 48.9 + - - +
1392 GLU* 4.5 12.3 + - - +
1402 PRO* 4.6 15.6 - - + +
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Residues in contact with ARG 140 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081 GLU* 4.1 26.7 - - + +
1391 ARG* 1.3 78.9 - - - +
1411 ALA* 1.3 57.4 + - - +
1431 ASP* 3.2 8.5 + - + +
1441 ARG* 2.9 63.7 + - + +
1402 PRO* 4.0 39.9 - - + +
1742 HIS* 6.2 2.8 - - - -
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Residues in contact with ALA 141 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041 ARG 4.2 2.0 - - - +
1071 LEU* 3.7 26.8 - - + +
1081 GLU* 3.6 32.7 + - + +
1341 VAL* 6.2 0.4 - - + -
1381 TYR* 4.3 21.5 - - + -
1391 ARG 3.3 1.0 - - - +
1401 ARG* 1.3 78.1 - - - +
1421 ALA* 1.3 57.8 + - - +
1441 ARG* 3.8 1.0 - - - +
1451 LEU* 2.9 35.5 + - - +
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Residues in contact with ALA 142 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1341 VAL* 4.2 19.2 - - + +
1381 TYR* 3.4 20.4 + - - +
1391 ARG 3.2 6.7 + - - +
1411 ALA* 1.3 80.5 - - - +
1431 ASP* 1.3 59.5 + - - +
1451 LEU* 3.6 9.3 - - - +
1461 GLU* 2.9 29.6 + - - +
1731 VAL* 5.1 7.3 - - + +
1751 ARG* 4.3 21.5 - - + +
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Residues in contact with ASP 143 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391 ARG* 2.6 63.0 + - - +
1401 ARG* 3.7 6.3 - - - +
1421 ALA* 1.3 79.4 - - - +
1441 ARG* 1.3 62.0 + - + +
1461 GLU* 3.4 6.3 + - - +
1471 GLN* 2.9 28.4 + - - +
1751 ARG* 5.6 3.1 + - - -
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Residues in contact with ARG 144 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271 TRP* 4.0 48.5 - - + +
1071 LEU 4.5 5.2 - - - +
1081 GLU* 3.8 25.0 + - - +
1111 PRO* 4.2 8.4 - - + +
1401 ARG* 2.9 45.2 + - + +
1411 ALA 4.0 3.4 - - - +
1431 ASP* 1.3 79.5 - - + +
1451 LEU* 1.3 57.8 + - - +
1471 GLN* 3.3 25.5 + - - +
1481 ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 145 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071 LEU* 4.3 27.4 - - + +
1111 PRO* 3.8 27.1 - - + +
1141 LEU* 4.6 14.4 - - + -
1151 ILE* 5.5 4.9 - - + -
1321 ILE* 4.3 20.4 - - + -
1341 VAL* 3.8 28.9 - - + -
1411 ALA 2.9 23.5 + - - +
1421 ALA* 3.6 5.8 - - - +
1441 ARG* 1.3 74.9 - - - +
1461 GLU* 1.3 59.9 + - - +
1481 ALA* 3.2 4.2 + - + +
1491 ILE* 2.9 39.8 + - + +
1731 VAL* 5.5 7.6 - - + -
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Residues in contact with GLU 146 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1421 ALA 2.9 16.2 + - - +
1431 ASP* 3.7 7.2 - - - +
1451 LEU* 1.3 75.9 - - - +
1471 GLN* 1.3 62.2 + - - +
1491 ILE* 3.4 4.3 + - - +
1501 LYS* 2.9 56.9 + - - +
1531 ARG* 4.1 16.8 + - - -
1731 VAL* 3.6 35.2 - - + +
172 LYS* 5.3 9.8 + - - -
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Residues in contact with GLN 147 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271 TRP* 4.1 23.3 + - - +
281 THR* 6.1 0.8 - - - +
1431 ASP 2.9 12.4 + - - +
1441 ARG* 3.3 39.5 + - - +
1451 LEU 3.2 0.2 - - - -
1461 GLU* 1.3 77.1 - - - +
1481 ALA* 1.3 63.0 + - - +
1501 LYS* 3.2 9.1 + - - +
1511 GLU* 2.9 46.8 + - + +
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Residues in contact with ALA 148 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271 TRP 5.9 0.7 - - - +
1111 PRO* 3.5 33.4 - - + -
1121 HIS* 3.4 31.9 - - + +
1151 ILE* 4.0 9.4 - - + -
1441 ARG 2.9 11.3 + - - +
1451 LEU* 3.2 4.7 + - - +
1471 GLN* 1.3 75.8 - - - +
1491 ILE* 1.3 64.5 + - - +
1511 GLU* 3.2 4.3 + - - -
1521 ALA* 2.9 22.3 + - - +
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Residues in contact with ILE 149 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151 ILE* 4.3 16.8 - - + -
1321 ILE* 4.5 10.3 - - + -
1451 LEU* 2.9 23.2 + - + +
1461 GLU* 3.9 5.6 - - - +
1481 ALA* 1.3 75.3 - - - +
1501 LYS* 1.3 64.3 + - - +
1521 ALA* 3.4 3.3 + - - +
1531 ARG* 2.9 57.2 + - + +
1581 LEU* 4.9 6.2 - - + +
1701 ASP* 4.7 1.3 - - - +
1711 LEU* 3.7 39.7 - - + +
1721 HIS 4.6 0.2 - - - +
1731 VAL* 3.6 29.8 - - + -
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Residues in contact with LYS 150 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1461 GLU* 2.9 50.2 + - + +
1471 GLN* 3.6 6.1 - - - +
1491 ILE* 1.3 77.5 - - - +
1511 GLU* 1.3 56.9 + - + +
1531 ARG* 3.3 17.2 + - - +
1541 ALA* 2.9 30.5 + - - +
132 GLU* 5.3 8.5 + - - -
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Residues in contact with GLU 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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271 TRP 3.9 11.1 - - - +
281 THR* 5.0 2.0 - - - -
291 LEU* 4.0 28.1 + - + +
1121 HIS* 3.8 21.9 + - + -
1471 GLN* 2.9 43.1 + - + +
1481 ALA* 3.2 6.1 + - - +
1501 LYS* 1.3 77.9 - - + +
1521 ALA* 1.3 63.9 + - - +
1541 ALA* 3.2 6.1 + - - +
1551 ARG* 3.0 31.1 + - + +
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Residues in contact with ALA 152 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291 LEU* 6.1 0.9 - - - -
381 TYR* 4.5 7.0 - - - +
1121 HIS* 4.4 12.2 - - + -
1151 ILE* 5.1 3.1 - - + -
1481 ALA 2.9 15.7 + - - +
1491 ILE 4.0 1.3 - - - +
1511 GLU* 1.3 77.5 - - - +
1531 ARG* 1.3 62.6 + - - +
1561 GLY 3.3 1.7 + - - -
1571 TYR* 2.8 53.2 + - + +
1581 LEU* 3.1 24.7 + - + -
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Residues in contact with ARG 153 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1461 GLU* 4.1 14.3 + - - -
1491 ILE* 2.9 46.5 + - + +
1501 LYS* 3.5 15.3 - - - +
1521 ALA* 1.3 76.9 - - - +
1541 ALA* 1.3 64.9 + - - +
1561 GLY* 3.7 5.4 + - - -
1581 LEU* 3.8 26.6 - - + +
1701 ASP* 4.2 26.4 + - - +
1711 LEU 4.2 6.8 + - - -
1721 HIS* 5.1 7.4 + - - +
1731 VAL* 5.9 0.2 - - - +
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Residues in contact with ALA 154 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1501 LYS 2.9 18.0 + - - +
1511 GLU* 3.2 5.6 + - - +
1531 ARG* 1.3 78.9 - - - +
1551 ARG* 1.3 61.0 + - + +
1561 GLY* 3.3 4.1 + - - -
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Residues in contact with ARG 155 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291 LEU* 3.4 31.6 - - + +
301 ASP* 4.2 22.0 + - - -
331 LEU* 5.1 4.8 - - - +
1511 GLU* 3.0 18.6 + - - +
1541 ALA* 1.3 78.4 - - + +
1561 GLY* 1.3 59.8 + - - +
1571 TYR* 3.5 22.0 + - + -
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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