Contacts of the helix formed by residues 108 - 115 (chain C) in PDB entry 1XGP
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C TRP* 4.1 12.1 - + - -
31C ALA* 5.4 4.0 - - + -
35C GLU* 3.4 27.6 - - + +
56C LEU* 3.1 41.5 + - + +
57C GLN 4.8 4.4 + - - -
58C ILE* 4.7 5.3 - - + +
95C ALA* 3.7 39.5 - - + -
98C ILE* 3.7 30.4 - - + +
99C VAL* 4.3 4.3 - - + -
105C MET* 3.0 55.8 + - + +
106C ASN 4.3 1.6 - - - -
107C ALA* 1.3 79.2 - - + +
109C VAL* 1.3 57.6 + - - +
110C ALA 3.1 1.1 - - - -
111C TRP* 2.7 43.0 + - + +
112C ARG* 3.2 5.2 + - - +
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU* 4.5 0.8 + - - -
107C ALA 3.3 7.1 + - - +
108C TRP* 1.3 71.3 - - - +
110C ALA* 1.3 63.3 + - - +
112C ARG* 3.2 42.1 + - - +
113C ASN* 3.1 41.1 + - - +
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ALA* 6.0 0.7 - - - -
34C PHE* 4.4 19.9 - - + +
35C GLU* 3.3 33.3 + - + +
108C TRP 3.1 0.8 - - - -
109C VAL* 1.3 80.7 - - - +
111C TRP* 1.3 61.7 + - - +
113C ASN* 4.2 5.7 - - - +
114C ARG* 3.1 26.5 + - - +
115C CYS* 4.1 3.2 + - - -
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Residues in contact with TRP 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 4.0 21.3 - + - -
27C ASN* 3.1 36.7 + - - -
31C ALA* 4.3 9.6 - - + +
105C MET* 3.2 59.2 - - + +
106C ASN* 3.5 24.9 - - - -
108C TRP* 2.7 33.7 + - + +
110C ALA* 1.3 71.3 - - - +
112C ARG* 1.3 66.9 + - + -
115C CYS* 2.7 37.9 + - + +
116C LYS* 2.6 64.7 + - + -
117C GLY 5.1 0.7 - - - -
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Residues in contact with ARG 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ASN* 2.6 63.6 + - - +
107C ALA 4.6 0.6 + - - -
108C TRP 3.9 7.0 - - - +
109C VAL* 3.2 47.3 + - - +
111C TRP* 1.3 84.2 - - + +
113C ASN* 1.3 71.6 + - - +
116C LYS* 3.3 38.2 + - + +
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Residues in contact with ASN 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 3.1 32.8 + - - +
110C ALA* 4.2 5.0 - - - +
112C ARG* 1.3 87.8 - - - +
114C ARG* 1.3 80.2 + - - +
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Residues in contact with ARG 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C CYS* 3.7 5.7 - - - -
34C PHE* 3.7 45.1 - - + -
110C ALA* 3.1 14.1 + - - +
113C ASN* 1.3 96.8 + - - +
115C CYS* 1.3 65.3 + - - +
116C LYS 5.4 0.2 - - - -
118C THR* 4.1 13.1 + - - +
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Residues in contact with CYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C CYS* 2.0 64.4 - - + -
31C ALA* 3.7 5.4 - - - -
34C PHE* 3.8 6.7 - - - -
110C ALA 4.4 0.7 - - - -
111C TRP* 2.7 40.7 + - + +
112C ARG 4.2 0.2 + - - -
113C ASN 3.8 0.2 - - - -
114C ARG* 1.3 76.1 - - - +
116C LYS* 1.3 66.6 + - - +
117C GLY 3.2 0.5 + - - -
118C THR* 2.8 27.2 + - - -
120C VAL* 3.4 10.3 - - + +
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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