Contacts of the strand formed by residues 103 - 106 (chain X) in PDB entry 4J5E
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 103 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97X ARG* 3.7 35.2 - - + +
98X VAL* 3.6 0.5 - - - +
99X ILE* 3.0 44.6 + - + +
102X PHE* 1.3 104.2 - - + +
104X CYS* 1.3 68.3 + - - +
105X GLN* 3.6 17.7 - - + -
155X PHE* 3.7 22.4 - - + -
156X ILE 3.3 13.7 - - - +
157X CYS* 4.0 2.9 - - - -
158X THR* 3.6 5.1 + - - +
301X 7B7 3.5 29.6 - - + -
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Residues in contact with CYS 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X PHE* 3.7 27.6 - - + -
97X ARG 3.9 3.4 - - - -
98X VAL* 4.0 4.9 - - + -
103X MET* 1.3 78.1 - - - +
105X GLN* 1.3 60.2 + - - +
155X PHE* 3.1 1.9 - - - -
156X ILE* 2.9 37.0 + - + +
158X THR* 4.3 3.4 - - - -
181X VAL* 4.0 20.4 - - + -
184X ILE* 3.7 23.6 - - + -
185X GLU* 3.8 25.8 - - - -
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Residues in contact with GLN 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95X PHE* 3.2 7.9 - - - -
96X HIS* 3.1 36.7 + - + -
97X ARG* 2.8 52.1 + - + +
103X MET* 3.6 8.7 - - - -
104X CYS* 1.3 72.8 - - - +
106X ALA* 1.3 64.0 + - - +
143X ALA* 3.6 15.6 - - + +
153X GLN* 2.9 25.4 + - - +
154X PHE 3.3 14.8 - - - +
155X PHE* 4.0 2.2 - - + -
301X 7B7 3.0 32.6 + - - +
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Residues in contact with ALA 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94X THR 3.3 17.9 - - - +
95X PHE* 3.6 24.0 - - + -
96X HIS* 4.1 7.6 - - - -
105X GLN* 1.3 76.1 - - - +
107X GLY* 1.3 61.2 + - - +
108X ASP 3.7 1.8 - - - -
153X GLN* 3.2 9.2 - - - +
154X PHE* 2.9 51.9 + - + -
200X ILE* 4.4 3.4 - - + -
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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