Contacts of the helix formed by residues 107 - 113 (chain B) in PDB entry 3P9I
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 PRO 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA* 4.3 17.1 - - + +
85B ASN 5.3 0.7 - - - +
88B THR* 5.5 2.5 - - + -
106B ALA* 1.3 91.1 - - + +
108B VAL* 1.3 61.9 + - - +
109B CYS 3.1 0.9 + - - -
110B LYS* 3.2 22.7 + - - +
111B PHE* 4.5 0.3 + - - -
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 3.4 26.8 - - + +
19A PHE* 3.4 41.3 - - + -
20A ALA* 3.5 19.5 - - + +
23A LEU* 4.0 5.2 - - + -
85B ASN 4.1 3.8 - - - +
86B VAL* 3.7 33.7 - - + +
106B ALA* 4.7 0.2 - - + -
107B PRO* 1.3 77.9 - - - +
109B CYS* 1.3 66.6 + - - +
110B LYS 3.1 0.4 - - - -
111B PHE* 2.9 13.6 + - - +
112B LEU* 3.4 12.2 + - + +
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Residues in contact with CYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 4.1 25.8 - - - -
45B LEU* 5.4 0.9 - - - -
46B VAL* 3.6 21.8 - - + -
86B VAL* 3.2 26.9 - - - -
87B VAL* 4.2 3.1 - - - -
105B ALA* 4.1 9.2 - - + -
106B ALA 3.1 24.1 + - - +
107B PRO 3.1 0.8 - - - -
108B VAL* 1.3 81.4 - - - +
110B LYS* 1.3 55.6 + - - +
112B LEU* 3.0 16.2 + - - -
113B THR* 2.7 31.0 + - + +
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASP* 2.5 32.0 + - - +
46B VAL* 4.9 2.4 - - - +
106B ALA 4.3 1.0 + - - -
107B PRO 3.2 14.8 + - - +
109B CYS* 1.3 79.2 - - - +
111B PHE* 1.3 76.9 + - + +
113B THR* 3.2 24.7 + - - +
114B PRO 5.2 0.5 - - - +
115B ASN* 5.0 9.1 - - + +
120B SER* 4.7 0.3 - - - -
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Residues in contact with PHE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASP* 3.0 51.4 - - + -
16A ALA* 3.4 18.2 - - + -
17A CYS* 3.3 38.4 - - + -
20A ALA* 3.5 17.5 - - + -
107B PRO 4.5 0.7 - - - -
108B VAL 2.9 6.8 + - - +
110B LYS* 1.3 100.4 - - + +
112B LEU* 1.3 60.0 + - - +
113B THR 3.6 0.9 - - - -
120B SER* 3.7 6.7 - - - +
121B MET* 2.9 34.7 + - + +
183B ILE* 5.9 7.6 - - + -
350B TYR* 4.5 6.7 - + - -
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA* 3.7 24.2 - - + +
23A LEU* 4.2 24.5 - - + -
24A ALA* 5.5 2.2 - - + -
33B LEU* 4.3 14.8 - - + -
37B ILE* 4.8 7.4 - - + +
42B LEU* 3.7 32.1 - - + +
43B GLU* 5.8 0.5 - - - +
86B VAL* 4.3 7.4 - - + -
108B VAL* 3.6 18.2 - - + +
109B CYS* 3.0 7.7 + - - +
111B PHE* 1.3 87.0 - - - +
113B THR* 1.3 65.7 + - - +
120B SER* 3.3 9.2 - - - -
121B MET* 4.2 9.4 - - + +
122B ALA* 3.6 24.6 - - + +
125B ALA* 5.6 1.1 - - + -
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 3.7 40.4 - - + +
43B GLU* 3.9 9.9 - - + +
46B VAL* 3.8 19.2 - - + +
109B CYS 2.7 22.0 + - - +
110B LYS* 3.2 17.8 + - - +
112B LEU* 1.3 85.8 - - - +
114B PRO* 1.3 80.2 + - - +
115B ASN 3.3 1.0 + - - -
119B VAL 3.8 0.3 - - - +
120B SER* 3.2 17.7 + - - -
122B ALA* 5.5 0.2 - - - -
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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