Contacts of the strand formed by residues 99 - 103 (chain E) in PDB entry 2XJZ
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 MET 99 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97E TYR 5.1 1.1 - - - +
98E GLU* 1.3 75.6 - - - +
100E THR* 1.3 61.1 + - - +
109E HIS* 4.1 4.0 - - - +
110E LEU* 3.3 43.7 + - + +
343M PRO* 3.9 27.6 - - + -
344M THR 3.7 6.7 - - - +
345M LEU* 4.8 10.8 - - + -
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Residues in contact with THR 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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94E ILE* 3.3 33.1 - - - +
99E MET* 1.3 69.6 + - - +
101E MET* 1.3 63.6 + - - +
102E ARG* 4.1 12.1 - - + +
107E VAL* 3.6 24.0 - - + +
108E TYR 3.4 11.0 + - - -
110E LEU* 4.3 2.5 - - - +
343M PRO* 3.3 9.5 - - - +
344M THR* 2.7 55.7 + - + +
346M MET* 4.1 12.2 - - - +
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Residues in contact with MET 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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100E THR* 1.3 71.4 - - - +
102E ARG* 1.3 62.8 + - - +
103E VAL* 4.6 1.6 - - + -
107E VAL* 3.7 0.2 - - - -
108E TYR* 2.9 44.4 + - - +
110E LEU* 3.7 28.2 - - + +
113E PHE* 3.6 44.4 - - + -
340M VAL* 4.1 16.8 - - + -
341M GLY 3.3 29.4 - - - +
342M GLU 4.3 2.9 - - - +
343M PRO* 3.6 24.7 - - + -
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Residues in contact with ARG 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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100E THR* 4.1 8.1 + - + +
101E MET* 1.3 74.6 - - - +
103E VAL* 1.3 65.5 + - - +
104E LYS 4.2 4.0 - - - +
106E LYS 3.7 5.8 - - - +
107E VAL* 3.8 18.0 - - + +
128E TYR* 5.1 0.5 + - - -
344M THR* 3.4 27.2 + - + +
345M LEU 3.2 23.2 + - - -
346M MET* 2.4 35.6 + - - +
349M GLU* 2.9 48.9 + - - +
350M PHE* 3.4 9.3 - - - -
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Residues in contact with VAL 103 (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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101E MET* 3.9 4.0 + - + +
102E ARG* 1.3 81.0 - - - +
104E LYS* 1.3 68.9 + - - +
106E LYS* 3.0 28.7 + - - +
108E TYR* 4.4 15.5 - - + -
113E PHE* 3.6 28.0 - - + -
128E TYR* 3.3 36.1 - - + +
130E LEU* 3.7 26.0 - - + -
135E ILE* 4.6 0.2 - - + -
338M MET* 4.2 11.0 - - - -
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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