Contacts of the strand formed by residues 54 - 58 (chain G) in PDB entry 4XLN
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 54 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G ALA 4.6 0.2 - - - -
53G VAL* 1.3 83.1 + - - +
55G SER* 1.3 58.3 + - - -
143G ARG* 2.6 16.1 + - - -
145G ASP* 2.8 39.6 + - + +
156G HIS* 3.7 16.5 - - + +
158G ILE* 3.6 26.7 - - + -
167G VAL* 3.1 39.7 + - - +
169G ALA* 5.7 2.0 - - - -
171G PHE* 6.0 0.2 - - - -
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Residues in contact with SER 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G VAL* 4.2 0.4 - - - +
54G THR* 1.3 80.1 - - - +
56G VAL* 1.3 76.5 + - - +
142G VAL* 3.2 5.9 - - - +
143G ARG* 2.9 30.1 + - - -
158G ILE* 3.5 41.4 - - - +
160G ASP* 4.1 8.7 + - - -
164G ALA* 4.2 1.4 - - - +
165G ILE 2.9 26.1 + - - -
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Residues in contact with VAL 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G VAL* 5.1 3.8 - - + -
55G SER* 1.3 85.3 + - - +
57G TYR* 1.3 71.5 - - - +
58G ILE* 4.7 4.7 - - + -
79G ILE* 5.2 4.0 - - + -
82G LEU* 3.6 31.9 - - + -
140G MET* 3.8 18.6 - - + -
141G GLU 3.4 11.9 - - - +
142G VAL* 3.6 19.7 - - + -
163G ASN 4.2 0.5 - - - +
164G ALA* 4.1 2.1 - - - +
165G ILE* 3.2 34.3 + - + +
167G VAL* 4.2 16.4 - - + -
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Residues in contact with TYR 57 (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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56G VAL* 1.3 77.4 - - - +
58G ILE* 1.3 93.7 + - - +
59G GLU* 3.7 19.5 + - + +
61G VAL 4.6 0.9 - - - -
139G TYR* 3.9 10.6 - + - +
140G MET* 3.6 1.0 - - - -
141G GLU* 2.9 56.2 + - + +
160G ASP* 6.5 0.9 - - + -
161G ARG* 3.1 46.6 - - - +
162G ILE* 5.5 2.2 - - + +
163G ASN* 3.0 45.3 + - + +
164G ALA* 5.3 2.5 - - + -
165G ILE* 6.3 1.1 - - - -
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Residues in contact with ILE 58 (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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56G VAL* 4.7 5.2 - - + -
57G TYR* 1.3 108.7 - - - +
59G GLU* 1.3 77.4 + - - +
60G ASP* 3.4 7.5 + - + +
61G VAL* 3.4 44.7 + - + +
68G ILE* 4.2 5.6 - - + -
75G VAL* 5.9 3.6 - - + -
138G LEU* 3.6 19.5 - - + -
139G TYR* 3.3 20.6 - - - +
140G MET* 3.6 33.9 - - + -
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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