Contacts of the helix formed by residues 99 - 107 (chain 0) in PDB entry 5OA3
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 TRP 99 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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980 THR* 1.3 84.1 + - - +
1000 PRO* 1.4 78.4 - - + +
1010 LEU* 3.4 48.5 - - + -
1020 VAL* 3.4 20.2 + - + +
1030 LEU* 3.6 2.4 + - - +
1160 GLY* 3.1 23.3 + - - +
1190 MET* 3.3 58.6 - - + +
1200 PRO* 4.3 1.6 - - + +
1210 PRO* 3.4 37.9 - - + +
1220 ALA* 3.8 2.2 - - - +
1370 LEU* 4.7 0.2 - - - +
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Residues in contact with PRO 100 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980 THR 4.0 4.0 - - - +
990 TRP* 1.4 103.5 - - + +
1010 LEU* 1.3 56.4 + - - +
1030 LEU* 2.9 38.9 + - + +
1040 GLU* 3.9 2.9 + - - +
1210 PRO* 4.3 14.4 - - + -
1370 LEU* 5.5 3.8 - - + -
1380 VAL* 5.4 7.9 - - + -
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Residues in contact with LEU 101 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990 TRP* 3.4 30.3 - - + -
1000 PRO* 1.3 77.6 - - - +
1020 VAL* 1.3 62.6 + - + +
1040 GLU* 4.2 7.8 + - - +
1050 LYS* 4.1 14.4 - - - +
1190 MET* 6.4 1.6 - - - -
761 A 3.5 49.9 - - + +
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Residues in contact with VAL 102 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980 THR* 4.4 1.8 - - - +
990 TRP* 3.6 21.3 - - + +
1010 LEU* 1.3 77.8 - - + +
1030 LEU* 1.3 53.9 + - - +
1050 LYS* 2.9 6.4 + - - -
1060 LEU* 2.6 49.1 + - + -
1120 LEU* 3.6 25.1 - - + -
1130 MET* 4.9 3.1 - - + +
1160 GLY* 3.8 27.4 - - - -
761 A 3.9 34.5 - - + +
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Residues in contact with LEU 103 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990 TRP 3.6 2.2 + - - -
1000 PRO* 2.9 21.5 + - + +
1020 VAL* 1.3 75.2 - - - +
1040 GLU* 1.3 66.7 + - - +
1060 LEU* 2.9 11.6 + - - +
1070 VAL* 2.8 40.8 + - + +
1370 LEU* 3.5 46.2 - - + -
1400 ASN* 5.6 0.7 - - - +
1440 VAL* 4.5 7.2 - - + -
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Residues in contact with GLU 104 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000 PRO 3.9 2.7 + - - +
1010 LEU* 4.5 7.2 - - - +
1020 VAL 3.1 1.0 + - - -
1030 LEU* 1.3 81.4 - - + +
1050 LYS* 1.3 75.5 + - + +
1070 VAL* 3.0 33.8 + - + +
1080 GLY* 3.1 5.5 + - - -
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Residues in contact with LYS 105 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010 LEU 4.1 9.9 - - - +
1020 VAL 2.9 6.4 + - - +
1040 GLU* 1.3 96.1 - - + +
1060 LEU* 1.3 60.7 + - - +
1080 GLY* 2.9 17.7 + - - +
1100 ALA* 3.2 23.7 + - + +
741 C 4.0 9.1 + - - -
761 A 3.4 80.9 + - + +
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Residues in contact with LEU 106 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980 THR* 3.3 32.3 - - + +
1020 VAL* 2.6 32.3 + - + +
1030 LEU* 3.1 14.4 - - - +
1050 LYS* 1.3 73.5 - - - +
1070 VAL* 1.3 58.5 + - - +
1080 GLY 3.2 0.4 + - - -
1090 GLY* 3.6 4.9 + - - -
1100 ALA 3.7 8.1 - - - +
1120 LEU* 3.9 18.6 - - + -
1350 ILE* 3.6 23.8 - - + -
1370 LEU* 4.7 3.4 - - + -
1440 VAL* 4.7 9.6 - - + -
1450 ALA* 5.0 3.6 - - + +
1680 VAL* 3.6 32.6 - - + +
1710 THR* 2.8 20.9 + - - -
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Residues in contact with VAL 107 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030 LEU* 2.8 34.6 + - + +
1040 GLU* 3.0 23.2 + - + +
1060 LEU* 1.3 77.5 - - - +
1080 GLY* 1.3 57.4 + - - +
1090 GLY 3.3 3.8 + - - -
1440 VAL* 4.6 13.2 - - + -
1710 THR* 3.5 15.5 - - - +
1720 TYR* 4.2 28.5 - - + +
1730 GLN* 5.4 6.1 - - - +
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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
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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