Contacts of the strand formed by residues 130 - 135 (chain E) in PDB entry 5JLH
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 ALA 130 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E PRO* 3.3 13.2 - - + +
102E VAL 3.0 21.2 + - - -
123E PHE* 4.4 4.0 - - - -
128E THR* 3.3 11.2 + - - -
129E PRO* 1.3 83.8 - - + +
131E MET* 1.3 63.6 + - - +
355E TRP* 3.8 23.8 - - + -
356E ILE 3.2 16.4 - - - +
357E SER* 4.1 4.5 - - - +
358E LYS 4.4 1.1 - - - +
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Residues in contact with MET 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E VAL* 3.0 23.6 - - + +
104E LEU* 3.9 20.4 - - + -
119E THR* 3.4 39.5 - - + +
122E MET* 3.7 16.4 - - + -
123E PHE* 3.5 22.0 - - + -
128E THR* 5.0 0.2 - - + -
130E ALA* 1.3 76.4 - - - +
132E TYR* 1.3 67.7 + - - +
133E VAL* 3.4 32.5 - - + -
355E TRP* 3.4 5.4 - - - -
356E ILE* 2.8 38.4 + - + +
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Residues in contact with TYR 132 (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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102E VAL 3.1 5.3 + - - +
103E LEU* 3.6 18.1 - - + +
104E LEU* 2.8 25.5 + - - +
131E MET* 1.3 82.0 - - - +
133E VAL* 1.3 85.1 + - - +
134E ALA* 3.5 15.2 - - + -
345E LEU* 5.1 4.3 - - + -
351E PHE* 3.7 27.4 - + + -
354E MET* 4.0 35.9 - - + +
355E TRP* 3.7 17.7 - - + -
356E ILE* 4.5 10.1 - - + -
372E LYS* 5.8 1.3 - - + -
373E CYS* 3.2 36.9 - - + +
374E PHE* 4.2 7.6 + - - +
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Residues in contact with VAL 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E LEU* 3.3 15.7 - - + +
106E GLU* 5.1 5.4 - - + -
115E ARG* 4.0 19.2 + - + +
118E MET* 4.2 16.8 - - + -
119E THR* 4.4 7.0 - - + -
131E MET* 3.4 27.6 - - + -
132E TYR* 1.3 85.6 - - - +
134E ALA* 1.3 60.2 + - - +
356E ILE* 4.9 2.3 - - + +
369E VAL* 3.3 32.8 - - + -
373E CYS* 3.6 16.7 - - - -
374E PHE* 4.2 4.5 - - - +
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Residues in contact with ALA 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E LEU* 3.8 13.0 - - + -
104E LEU 2.8 7.5 + - - +
105E THR* 3.4 2.8 - - - -
106E GLU* 2.8 28.9 + - - +
115E ARG* 6.1 1.1 - - - -
132E TYR* 3.5 23.6 - - + -
133E VAL* 1.3 76.0 - - - +
135E ILE* 1.3 62.6 + - - +
139E LEU* 3.7 24.5 - - + -
345E LEU* 5.1 3.4 - - + -
374E PHE* 5.4 2.0 - - - -
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Residues in contact with ILE 135 (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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105E THR* 4.2 0.4 - - - -
106E GLU 3.4 1.8 - - - +
107E ALA 3.9 1.6 - - - -
108E PRO* 3.4 50.5 - - + -
109E LEU 5.0 0.2 - - - +
115E ARG* 3.6 23.8 - - - +
134E ALA* 1.3 72.6 - - - +
136E GLN* 1.3 64.2 + - - +
137E ALA* 4.1 2.7 - - + +
138E VAL* 3.2 40.4 - - + +
139E LEU* 3.2 19.8 + - - +
162E VAL* 5.3 5.4 - - + -
374E PHE* 4.4 35.1 + - + +
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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