Contacts of the helix formed by residues 98 - 102 (chain E) in PDB entry 1XBT
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 GLU 98 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E LYS* 6.5 0.2 - - - +
54E LYS* 3.9 14.0 - - + -
55E TYR* 4.3 7.6 - - + +
58E ASP* 2.8 41.9 - - - +
60E ARG* 3.7 8.3 + - - -
97E ASP* 1.3 88.1 + - - +
99E GLY* 1.3 64.2 - - - +
100E GLN* 3.0 19.3 + - - +
101E PHE* 3.2 42.0 + - + +
102E PHE* 3.9 5.7 - - - -
122E ALA 3.0 9.8 + - - -
123E ALA* 4.7 0.4 - - - +
5195E TTP 3.6 29.5 + - - +
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Residues in contact with GLY 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ILE* 4.1 3.1 - - - +
97E ASP 3.4 1.4 - - - -
98E GLU* 1.3 74.2 - - - +
100E GLN* 1.3 60.8 + - - +
101E PHE 3.1 1.8 + - - -
102E PHE* 3.3 18.2 + - - +
105E ILE* 3.8 39.1 - - - +
121E VAL* 4.1 9.6 - - - -
122E ALA 2.9 13.4 + - - -
123E ALA* 4.1 2.5 - - - -
136E ILE* 4.4 3.8 - - - -
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Residues in contact with GLN 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E GLU* 3.2 22.9 - - - +
99E GLY* 1.3 75.7 - - - +
101E PHE* 1.3 83.4 + - + +
102E PHE 3.4 3.4 + - - +
123E ALA* 3.3 7.0 - - + +
124E LEU* 3.1 51.5 + - - +
133E PHE* 3.6 65.0 - - + +
134E GLY* 4.4 7.8 - - - -
135E ALA 5.0 1.4 + - - -
136E ILE* 4.2 8.5 - - + +
5195E TTP 4.0 5.3 + - - -
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Residues in contact with PHE 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E TYR* 3.4 51.1 + + + -
79E CYS 4.5 0.7 - - - +
98E GLU* 3.2 29.5 + - - +
99E GLY 3.1 1.6 - - - -
100E GLN* 1.3 91.8 - - - +
102E PHE* 1.3 60.8 + - - +
103E PRO* 3.3 11.8 - - - +
133E PHE* 3.6 28.3 - + - -
173E GLU* 3.7 35.7 - - + -
175E ILE* 4.1 9.2 - - + -
5195E TTP 3.3 37.7 - - - -
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Residues in contact with PHE 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ILE* 4.0 11.2 - - + -
54E LYS 3.9 4.0 - - - -
55E TYR* 3.7 20.2 - + + -
78E ALA* 3.4 39.5 - - + -
79E CYS* 3.5 18.2 - - - -
80E LEU* 4.1 0.4 - - - -
81E LEU* 3.7 36.8 - - + -
96E ILE* 3.8 20.6 - - + -
97E ASP 3.8 21.5 - - - -
98E GLU 3.9 11.4 - - - -
99E GLY* 3.3 11.1 + - - +
100E GLN 3.4 3.6 - - - +
101E PHE* 1.3 79.7 - - - +
103E PRO* 1.3 68.1 - - - +
104E ASP* 3.2 3.2 + - - +
105E ILE* 3.2 19.9 + - + +
135E ALA* 5.4 1.9 + - - +
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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