Contacts of the strand formed by residues 128 - 131 (chain G) in PDB entry 4XLQ
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 HIS 128 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G GLU* 5.9 1.7 - - - +
81G ASN* 2.9 34.0 - - - +
108G GLU* 3.0 30.1 + - + +
109G VAL 3.5 7.4 + - - -
110G ARG* 4.5 8.5 - - + +
126G ASP 3.2 6.7 + - - +
127G LEU* 1.3 73.6 - - + +
129G ILE* 1.3 69.6 + - - +
130G ALA* 3.5 22.3 + - - -
131G THR* 3.1 24.2 + - - -
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Residues in contact with ILE 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G GLU* 3.9 4.9 - - - +
78G ILE* 3.5 29.6 - - + +
81G ASN* 3.2 32.3 + - + +
82G LEU* 3.9 22.2 - - + -
85G LEU* 5.4 3.4 - - + -
101G LEU* 4.6 1.1 - - + -
109G VAL* 2.5 31.7 + - + +
110G ARG 3.4 26.5 - - - +
111G ALA* 4.2 8.3 - - + +
114G PHE* 4.6 11.0 - - + -
127G LEU* 4.1 9.0 - - + +
128G HIS* 1.3 75.6 - - - +
130G ALA* 1.3 63.7 + - + +
138G LEU* 5.0 0.2 - - + -
140G MET* 4.1 15.0 - - + -
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Residues in contact with ALA 130 (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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71G VAL* 3.7 27.4 - - + -
73G GLU* 4.0 8.1 - - + -
78G ILE* 3.8 15.0 - - + -
109G VAL* 2.9 34.7 + - + +
128G HIS* 3.5 8.6 + - - -
129G ILE* 1.3 84.7 - - + +
131G THR* 1.3 61.6 + - - +
132G LEU* 3.8 9.4 - - + -
138G LEU* 4.8 2.2 - - + -
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Residues in contact with THR 131 (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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70G GLY 4.0 0.2 - - - +
72G LYS* 3.1 51.5 + - + +
73G GLU* 3.1 15.8 + - - -
108G GLU* 3.2 26.7 + - - +
128G HIS* 3.1 19.3 + - - -
130G ALA* 1.3 69.5 - - - +
132G LEU* 1.3 63.5 + - - +
133G GLU 4.1 0.3 + - - -
644I ARG* 6.3 0.4 - - - -
645I VAL* 3.8 28.2 - - + +
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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