Contacts of the helix formed by residues 108 - 115 (chain L) in PDB entry 1JTO
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 108 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ALA* 3.4 23.0 - - + +
105A SER* 3.8 2.9 - - - -
28L TRP* 3.8 11.0 - + - -
31L ALA* 4.9 3.8 - - + -
35L GLU* 3.7 25.1 - - + +
56L LEU* 2.8 45.0 + - + +
58L ILE* 5.0 1.1 - - + -
95L ALA* 3.6 45.5 - - + -
98L ILE* 4.2 13.5 - - + -
99L VAL* 3.5 22.7 - - + -
104L GLY 4.4 4.9 - - - -
105L MET* 3.3 27.3 + - + +
106L ASN 3.0 7.6 - - - +
107L ALA* 1.3 76.1 - - + +
109L VAL* 1.3 67.1 + - - +
110L ALA 3.2 0.2 - - - -
111L TRP* 3.0 26.3 + - + +
112L ARG 3.1 9.4 + - - -
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Residues in contact with VAL 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A TYR* 4.5 6.5 - - + -
105A SER* 3.3 19.5 + - - +
106A TYR 3.3 25.4 - - - +
107A TYR* 4.0 28.9 - - + -
111A HIS* 5.7 4.0 - - - +
35L GLU* 4.6 0.4 - - - +
107L ALA 3.5 1.2 + - - +
108L TRP* 1.3 70.5 - - - +
110L ALA* 1.3 64.9 + - - +
112L ARG* 3.1 14.9 + - - +
113L ASN* 3.0 47.5 + - - +
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Residues in contact with ALA 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L ALA* 4.4 1.6 - - - +
34L PHE* 3.5 31.9 - - + +
35L GLU* 3.2 33.9 + - + +
109L VAL* 1.3 79.4 - - - +
111L TRP* 1.3 56.7 + - - +
113L ASN* 4.6 4.3 - - - +
114L ARG* 2.8 36.7 + - - +
115L CYS* 4.4 0.6 - - - -
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Residues in contact with TRP 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L TYR* 4.3 14.1 - + - -
27L ASN* 3.0 48.8 + - - +
31L ALA* 4.0 9.5 - - + +
105L MET* 2.8 57.4 - - + +
106L ASN* 3.8 20.4 - - - -
108L TRP* 3.0 19.3 + - + +
110L ALA* 1.3 78.8 - - - +
112L ARG* 1.3 71.7 + - - +
115L CYS* 2.9 34.7 + - + +
116L LYS* 2.8 64.4 + - + -
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Residues in contact with ARG 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A TYR* 3.5 31.1 + - - -
107A TYR* 3.9 17.0 + - - -
118A TYR* 3.1 45.6 - - + +
119A GLY* 5.7 0.6 - - - -
106L ASN* 3.0 50.7 + - - +
108L TRP 3.1 3.6 + - - +
109L VAL* 3.1 21.0 + - - +
111L TRP* 1.3 90.5 - - + +
113L ASN* 1.3 64.4 + - - +
116L LYS* 3.8 21.6 + - + +
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Residues in contact with ASN 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A HIS* 4.5 20.5 - - - -
109L VAL* 3.0 44.6 + - - +
110L ALA* 4.1 3.7 - - - +
112L ARG* 1.3 85.5 - - - +
114L ARG* 1.3 87.8 + - + +
115L CYS 3.9 0.2 - - - -
116L LYS 5.9 0.4 - - - -
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Residues in contact with ARG 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L CYS* 3.8 3.5 - - - -
34L PHE* 3.4 43.2 - - + -
110L ALA* 2.8 19.9 + - - +
113L ASN* 1.3 96.5 + - + +
115L CYS* 1.3 60.5 + - - +
116L LYS 5.3 0.2 - - - -
118L THR* 4.0 6.0 - - - +
3M PHE 4.8 3.4 + - - -
4M GLY* 3.9 5.7 - - - -
5M ARG* 2.9 77.6 + - - +
33M LYS* 5.4 4.9 - - - +
38M PHE* 3.7 26.2 - - - -
123M TRP* 5.4 3.8 - - - -
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Residues in contact with CYS 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L CYS* 2.0 64.6 - - + -
31L ALA* 3.6 3.1 - - - -
34L PHE* 4.2 3.8 - - - -
110L ALA 4.4 0.9 - - - -
111L TRP* 2.9 37.6 + - + +
113L ASN 3.9 0.4 - - - -
114L ARG* 1.3 81.9 - - - +
116L LYS* 1.3 67.9 + - - +
117L GLY 3.2 0.3 + - - -
118L THR* 2.8 26.4 + - - -
120L VAL* 3.3 12.9 - - + +
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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