Contacts of the helix formed by residues 143 - 155 (chain 6) in PDB entry 5OOM
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 CYS 143 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1396 TRP* 3.6 10.0 + - - -
1426 THR* 1.3 85.4 + - - +
1446 GLY* 1.3 65.9 + - - +
1456 PRO* 3.3 2.9 - - - -
1466 TYR* 3.3 24.8 + - + +
1476 HIS* 3.5 26.5 + - + +
109P GLU* 3.2 42.2 - - - -
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Residues in contact with GLY 144 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1396 TRP* 3.0 45.9 + - - +
1406 GLU* 5.1 1.6 - - - -
1436 CYS* 1.3 76.7 - - - +
1456 PRO* 1.3 60.7 - - - +
1476 HIS* 3.1 2.4 + - - +
1486 LYS* 2.9 38.5 + - - +
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Residues in contact with PRO 145 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1406 GLU 4.5 7.4 - - - +
1416 ARG 4.4 8.1 - - - +
1426 THR 3.8 14.4 - - - +
1436 CYS 3.5 4.3 - - - -
1446 GLY* 1.3 88.2 - - - +
1466 TYR* 1.3 60.6 + - + +
1486 LYS* 3.5 2.3 + - + -
1496 GLN* 3.0 22.5 + - - +
1686 VAL* 3.7 19.5 - - + +
1696 PRO* 3.3 43.0 - - + +
1706 ARG* 4.2 21.1 - - - +
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Residues in contact with TYR 146 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1426 THR 4.7 9.6 - - - -
1436 CYS* 3.3 24.0 + - + +
1456 PRO* 1.3 79.7 - - + +
1476 HIS* 1.3 64.9 + - + +
1496 GLN* 3.2 22.8 + - - +
1506 ARG* 3.0 28.1 + - - +
1686 VAL* 4.3 17.3 - - + -
1706 ARG* 3.2 33.3 + - - -
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Residues in contact with HIS 147 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1396 TRP* 3.0 32.3 + - + -
1436 CYS* 3.5 27.5 + - - +
1446 GLY 3.1 7.5 + - - +
1466 TYR* 1.3 83.2 - - + +
1486 LYS* 1.3 59.8 + - - +
1496 GLN 3.1 0.2 - - - -
1506 ARG* 3.1 30.6 + - - +
1516 LEU* 3.0 35.7 + - + +
102P VAL 4.9 0.3 - - - +
104P SER* 3.9 20.6 + - - -
105P ALA* 5.8 0.2 - - - -
109P GLU* 4.3 7.0 - - - -
135P ARG* 3.1 19.2 + - - -
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Residues in contact with LYS 148 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1366 ARG* 6.0 0.7 - - - +
1396 TRP* 4.7 15.5 - - + -
1406 GLU* 4.0 23.9 + - - -
1446 GLY* 2.9 23.0 + - - +
1456 PRO* 5.1 0.9 - - + -
1476 HIS* 1.3 72.6 - - - +
1496 GLN* 1.3 59.8 + - - +
1516 LEU* 3.8 8.1 - - - +
1526 ALA* 3.0 29.1 + - - +
1586 TYR* 4.7 0.2 + - - -
1696 PRO* 3.7 26.5 - - + +
1716 VAL 5.0 2.4 + - - +
1726 PRO* 4.6 9.7 - - - +
1736 LEU 4.3 13.5 + - - +
1886 TYR* 6.3 1.9 - - - +
1896 CYS* 3.9 31.4 - - + +
3166 LEU* 4.5 23.5 + - + +
3176 SER* 6.0 1.4 - - - -
3186 PHE* 4.6 3.2 - - + -
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Residues in contact with GLN 149 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456 PRO 3.0 14.0 + - - +
1466 TYR* 3.3 22.3 - - - +
1476 HIS 3.1 0.2 - - - -
1486 LYS* 1.3 74.4 - - - +
1506 ARG* 1.3 59.2 + - - +
1526 ALA* 3.4 1.2 + - - +
1536 GLU* 2.9 52.0 + - - +
1586 TYR* 4.0 12.3 - - + -
1666 THR* 4.1 14.5 + - - -
1676 PHE* 3.5 26.1 + - - +
1686 VAL* 3.3 20.1 - - - +
1696 PRO* 4.3 2.9 - - + +
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Residues in contact with ARG 150 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1466 TYR 3.0 17.2 + - - +
1476 HIS* 3.1 27.4 + - - +
1496 GLN* 1.3 77.5 - - - +
1516 LEU* 1.3 58.7 + - - +
1536 GLU* 3.3 10.1 + - - +
1546 TYR* 2.9 29.8 + - - +
93P LEU* 5.6 1.6 - - - +
101P VAL* 3.9 35.6 + - - +
102P VAL 4.0 13.0 - - - +
104P SER* 2.4 41.0 + - - +
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Residues in contact with LEU 151 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1396 TRP* 6.0 2.2 - - + -
1476 HIS* 3.0 21.7 + - + +
1486 LYS* 3.4 4.2 + - + +
1496 GLN 3.3 0.2 - - - -
1506 ARG* 1.3 76.6 - - - +
1526 ALA* 1.3 58.3 + - - +
1546 TYR* 4.4 1.1 - - - +
1556 TYR* 3.1 39.4 + - + +
1896 CYS* 3.6 30.1 - - + +
3186 PHE* 3.6 20.5 - - + -
102P VAL* 3.5 39.9 - - + +
103P VAL* 3.9 15.9 - - + -
138P GLU* 4.9 5.8 - - - +
139P ALA* 4.1 13.2 - - + -
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Residues in contact with ALA 152 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486 LYS 3.0 17.9 + - - +
1506 ARG 3.2 0.2 - - - -
1516 LEU* 1.3 77.2 - - - +
1536 GLU* 1.3 61.8 + - - +
1556 TYR 4.6 0.2 - - - +
1566 GLY 3.3 1.2 + - - -
1576 LEU* 2.9 39.6 + - + +
1586 TYR* 3.6 34.7 + - + +
3166 LEU* 3.7 15.3 - - + -
3186 PHE* 3.9 9.4 - - + -
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Residues in contact with GLU 153 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1496 GLN* 2.9 47.9 + - - +
1506 ARG* 3.8 9.8 - - - +
1526 ALA* 1.3 76.4 - - - +
1546 TYR* 1.3 63.1 + - - +
1566 GLY* 3.4 10.9 + - - +
1586 TYR* 3.6 20.4 - - + -
1666 THR* 3.9 15.6 - - + +
100P LYS* 4.2 16.3 + - + -
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Residues in contact with TYR 154 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1506 ARG 2.9 17.4 + - - +
1516 LEU* 4.1 2.7 - - - +
1536 GLU* 1.3 79.0 - - - +
1556 TYR* 1.3 94.8 + + - +
1566 GLY 3.2 1.3 + - - -
53P PRO* 3.8 19.1 + - + +
54P ARG* 4.7 12.0 + - + +
57P GLU* 3.4 8.7 + - - -
79P HIS* 3.0 37.5 + + - -
96P HIS* 3.3 44.2 + + + -
98P ASN* 4.8 0.4 - - - -
100P LYS* 4.2 28.6 + - + -
101P VAL 5.3 1.1 - - - +
102P VAL* 3.6 30.7 - - + -
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Residues in contact with TYR 155 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1516 LEU* 3.1 23.4 + - + +
1536 GLU 3.3 0.2 - - - -
1546 TYR* 1.3 102.3 - + - +
1566 GLY* 1.3 62.4 + - - +
1576 LEU* 3.3 15.6 + - + -
1896 CYS 5.4 0.7 - - - -
1906 GLY* 3.5 19.8 + - - -
2676 ARG* 3.1 24.2 + - + -
3186 PHE* 3.4 19.3 - + - -
3206 GLN* 3.1 26.7 + - - -
52P ASN* 5.0 4.9 - - - -
53P PRO* 3.2 15.7 - - + +
54P ARG* 3.3 35.6 + - + -
102P VAL* 5.2 4.0 - - + -
139P ALA 2.4 30.3 + - - -
141P ILE* 4.6 0.6 - - + +
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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
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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