Contacts of the strand formed by residues 126 - 129 (chain L) in PDB entry 3IT8
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 ARG 126 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120L TYR* 3.7 8.5 - - - -
121L HIS* 3.0 27.0 + - - +
124L ASP* 3.6 40.1 + - + +
125L LYS* 1.3 79.0 - - - +
127L PHE* 1.3 71.7 + - - +
128L THR* 4.7 5.3 + - - +
143L VAL* 5.2 8.1 - - + -
148L TRP* 4.0 14.1 - - + -
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Residues in contact with PHE 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L GLY 4.7 2.0 - - - -
109L TYR* 4.9 0.2 - - - -
110L VAL* 4.0 23.8 - - + -
118L ALA* 3.8 18.2 - - + -
119L ARG 3.3 19.3 - - - -
120L TYR* 3.7 19.7 - + + -
126L ARG* 1.3 85.3 + - - +
128L THR* 1.3 63.5 + - - +
135L PHE* 3.8 28.2 - - + -
140L MET* 3.5 24.0 - - - -
141L LEU* 3.9 20.1 + - + +
148L TRP* 3.7 24.5 - + - -
151L VAL* 4.3 5.6 - - + -
155L LEU* 3.6 23.6 - - + -
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Residues in contact with THR 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L ALA* 3.5 0.3 - - - -
119L ARG* 2.7 35.2 + - - +
121L HIS* 3.0 36.8 - - + +
124L ASP* 4.9 1.7 + - - -
126L ARG* 4.3 10.7 + - - +
127L PHE* 1.3 77.7 + - - +
129L LYS* 1.3 83.4 + - + +
135L PHE* 3.7 5.6 - - - -
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Residues in contact with LYS 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L LEU 3.9 1.1 - - - -
119L ARG* 4.4 5.0 + - - -
128L THR* 1.3 88.4 - - + +
130L MET* 1.3 61.0 + - - +
131L THR 3.3 18.8 - - - +
132L HIS* 3.3 31.9 + - - +
134L GLY* 4.0 18.6 - - - -
135L PHE* 3.5 20.1 - - + -
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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