Contacts of the helix formed by residues 102 - 108 (chain K) in PDB entry 1IA0
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 GLY 102 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100K GLY 3.3 0.4 - - - -
101K ALA* 1.3 82.0 - - - +
103K LYS* 1.3 64.1 + - - +
104K SER 3.6 1.8 - - - -
105K TYR* 3.8 1.7 + - - +
106K THR* 3.1 27.4 + - - -
330K ALA* 3.8 7.0 - - - +
503K ACP 3.0 38.1 + - - -
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Residues in contact with LYS 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K ALA* 3.9 17.0 - - + +
96K TYR* 3.8 18.8 - - - +
97K GLY* 3.1 27.8 + - - +
98K GLN 3.0 20.0 + - - -
102K GLY* 1.3 73.9 - - - +
104K SER* 1.3 59.7 + - - +
106K THR* 3.4 3.5 + - - -
107K MET* 3.0 33.6 + - - +
248K ASP* 3.4 12.3 - - - +
249K LEU 2.9 28.7 - - - +
250K ALA 3.8 6.5 - - - +
251K GLY* 3.8 1.0 - - - -
330K ALA* 4.1 10.5 - - + -
503K ACP 2.6 52.6 + - - +
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Residues in contact with SER 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K LYS* 1.3 71.1 - - - +
105K TYR* 1.3 58.3 + - - +
108K MET* 2.6 38.0 + - - +
109K GLY 2.9 5.0 + - - -
203K ARG* 4.6 4.3 + - - -
248K ASP* 2.6 23.2 + - - -
501K MG 2.0 29.4 - - - -
503K ACP 2.8 18.2 + - - -
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Residues in contact with TYR 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K ARG* 4.0 4.5 - - - -
67K TYR* 4.2 4.7 + - - -
70K GLN* 2.9 56.6 + - + +
102K GLY 4.0 1.8 - - - +
103K LYS 3.3 0.2 - - - -
104K SER* 1.3 75.2 - - - +
106K THR* 1.3 61.2 + - - +
109K GLY* 2.9 22.3 + - - +
110K LYS* 4.0 17.3 - - + -
115K GLN* 3.1 34.8 - - + +
503K ACP 2.8 100.2 + + + +
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Residues in contact with THR 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K ARG* 3.1 37.7 + - - +
70K GLN* 4.4 2.1 + - - +
73K VAL* 4.4 6.4 - - + +
95K ALA* 5.2 2.0 - - + -
102K GLY 3.1 17.7 + - - -
103K LYS* 3.7 5.2 - - - -
104K SER 3.2 0.6 - - - -
105K TYR* 1.3 80.3 - - - +
107K MET* 1.3 64.4 + - + +
117K GLY* 3.5 3.5 - - - -
118K ILE* 3.0 41.3 + - + +
328K VAL* 3.9 27.9 - - + +
503K ACP 5.5 0.2 + - - -
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Residues in contact with MET 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93K ILE* 3.9 26.0 - - + +
95K ALA* 3.3 35.0 - - + -
103K LYS 3.0 9.9 + - - +
104K SER 4.2 0.4 - - - +
106K THR* 1.3 80.9 - - - +
108K MET* 1.3 58.9 + - + +
118K ILE* 3.3 27.8 + - + +
119K ILE* 2.9 60.1 + - + +
120K PRO* 3.5 0.5 - - - +
246K LEU* 4.2 5.4 - - + -
247K VAL 3.8 25.1 - - - +
248K ASP* 4.4 13.2 - - + -
328K VAL* 5.5 1.1 - - - -
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Residues in contact with MET 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K SER* 2.6 21.7 + - - +
107K MET* 1.3 73.9 - - + +
109K GLY* 1.3 65.9 + - - +
110K LYS 3.8 1.2 + - - +
116K GLN* 3.7 1.0 - - - -
117K GLY 2.7 24.0 + - - -
119K ILE* 4.0 20.0 - - + -
120K PRO* 3.4 22.2 - - - +
146K TYR* 3.4 13.7 - - + +
193K GLN* 5.5 0.9 - - - -
196K MET* 3.5 35.2 - - + +
200K ASN* 3.2 41.1 - - - +
221K PHE* 5.6 0.2 - - + -
248K ASP* 5.8 1.6 - - - +
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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