Contacts of the strand formed by residues 105 - 110 (chain C) in PDB entry 3JRS
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 THR 105 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C PHE* 3.7 3.3 - - - -
94C VAL* 3.5 17.2 - - - +
95C SER 5.4 0.5 + - - -
98C PHE* 3.7 7.8 - - - -
103C GLY 4.1 7.9 - - - +
104C CYS* 1.3 78.7 - - - +
106C ARG* 1.3 63.0 + - - +
120C ARG* 4.0 34.3 + - - +
121C GLU 3.1 14.6 - - - +
122C ARG* 4.5 11.4 - - + -
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Residues in contact with ARG 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ARG 4.9 0.2 + - - -
79C PHE* 2.8 72.9 + - + +
82C PRO* 3.8 18.9 - - - +
86C LYS* 3.4 23.0 - - - +
92C CYS* 3.7 23.8 - - - -
93C ASN 3.3 8.3 - - - +
94C VAL* 3.8 5.6 - - + -
105C THR* 1.3 76.6 - - - +
107C ASP* 1.3 62.4 + - - +
108C VAL* 4.1 7.7 - - + +
119C SER 3.6 0.5 - - - +
120C ARG* 3.5 6.8 - - - -
121C GLU* 2.8 63.2 + - + +
135C PHE* 3.8 21.4 - - - -
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Residues in contact with ASP 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C CYS* 3.4 1.7 - - - -
93C ASN* 2.7 57.1 + - + +
106C ARG* 1.3 74.1 - - - +
108C VAL* 1.3 62.3 + - - +
109C ASN* 4.3 2.0 + - - +
118C THR* 4.5 9.6 + - - +
119C SER 3.2 5.5 - - - +
120C ARG* 3.1 49.0 + - - +
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Residues in contact with VAL 108 (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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3C A8S 5.0 2.5 - - - +
82C PRO* 3.6 30.1 - - + -
89C ILE* 3.9 23.8 - - + -
91C SER 3.4 5.2 - - - +
92C CYS* 4.0 11.0 - - + -
106C ARG* 4.1 14.1 - - - +
107C ASP* 1.3 76.2 - - - +
109C ASN* 1.3 61.8 + - - +
110C VAL* 4.8 7.7 - - + +
118C THR* 3.1 8.8 + - - -
119C SER* 2.9 57.1 + - - +
121C GLU* 4.0 10.8 - - - +
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Residues in contact with ASN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ILE* 3.4 4.9 - - - -
90C LYS* 2.8 31.3 + - + -
91C SER* 2.7 44.0 + - - +
93C ASN* 3.4 24.3 + - - +
107C ASP* 4.3 3.0 + - - +
108C VAL* 1.3 79.4 - - - +
110C VAL* 1.3 61.9 + - - +
117C ASN 3.8 4.7 - - - +
118C THR* 4.1 12.3 + - - -
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C A8S 3.8 38.1 - - + +
88C PHE 3.1 14.8 - - - +
89C ILE* 4.1 13.2 - - + -
90C LYS* 3.9 9.1 - - - +
108C VAL* 4.8 5.6 - - + +
109C ASN* 1.3 77.8 - - - +
111C ILE* 1.4 71.4 + - - +
112C SER 3.7 0.3 + - - -
114C LEU* 4.3 11.7 - - + -
116C ALA 3.2 27.6 - - - +
117C ASN* 3.1 23.7 + - - +
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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
------------------------------------------------------------
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