Contacts of the strand formed by residues 131 - 136 (chain G) 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 131 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ARG* 3.5 52.0 + - - +
45G ASP* 3.8 14.4 + - - +
47G GLN* 3.0 32.9 + - + +
48G LEU 3.5 5.2 - - - +
49G VAL* 4.2 13.7 - - + +
82G ARG* 3.5 3.1 - - - -
83G ILE* 3.0 63.4 + - + +
129G GLY 4.1 8.5 + - - +
130G ASP* 1.3 75.4 - - - +
132G LEU* 1.3 62.0 + - - +
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Residues in contact with LEU 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G GLN* 3.2 8.4 - - - +
48G LEU* 2.8 38.4 + - + +
50G VAL* 4.2 7.0 - - + -
58G ILE* 3.6 33.7 - - + -
80G ILE* 4.9 3.4 - - + -
81G SER 3.3 12.1 - - - +
82G ARG* 4.0 17.7 - - + -
93G LEU* 4.1 4.7 - - + -
126G LEU* 3.9 21.8 - - + -
130G ASP* 5.2 1.1 - - + -
131G ARG* 1.3 78.8 - - - +
133G SER* 1.3 61.2 + - - +
152G PHE* 3.9 18.0 - - + -
154G ILE* 3.8 30.7 - - + -
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Residues in contact with SER 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ASN 5.2 2.0 - - - -
47G GLN* 2.9 31.7 + - - +
79G THR 3.6 0.6 - - - +
80G ILE* 3.0 8.3 - - - +
81G SER* 2.8 36.7 + - - -
83G ILE* 4.4 6.6 - - - +
90G LYS* 4.0 10.4 + - - -
132G LEU* 1.3 75.0 - - - +
134G ALA* 1.3 60.9 + - - +
135G GLU* 3.5 27.2 + - - -
152G PHE* 4.1 3.1 - - - -
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Residues in contact with ALA 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G LEU* 3.9 5.8 - - - +
28G TRP* 3.5 31.4 + - + +
46G ASN* 5.3 2.5 + - - -
60G SER* 4.0 13.5 - - - +
78G HIS* 4.5 5.2 - - - +
79G THR 3.6 4.9 - - - -
80G ILE* 4.4 3.4 - - + -
133G SER* 1.3 72.9 - - - +
135G GLU* 1.3 62.3 + - - +
152G PHE* 3.5 43.5 - - + -
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Residues in contact with GLU 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LEU* 4.8 2.2 - - - -
46G ASN* 6.0 4.0 - - - +
47G GLN* 4.8 2.3 + - - +
78G HIS* 3.4 5.9 - - - -
79G THR* 3.0 40.9 + - + +
81G SER* 5.1 2.2 + - - -
90G LYS* 3.1 39.4 + - - +
133G SER* 3.5 15.3 - - - -
134G ALA* 1.3 79.1 - - - +
136G ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LEU* 4.0 14.3 - - + +
62G VAL* 3.7 28.5 - - + -
64G PHE* 3.8 21.8 - - + -
77G THR* 3.2 17.3 - - - +
78G HIS* 4.0 3.1 - - + -
79G THR* 6.2 0.2 - - - -
135G GLU* 1.3 83.2 - - - +
137G ASN* 1.3 61.3 + - - +
139G PRO* 3.5 32.5 - - + +
142G LEU* 3.5 37.7 - - + -
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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
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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