Contacts of the helix formed by residues 81 - 88 (chain K) 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 PRO 81 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1495J ILE* 4.2 7.7 - - + +
79K LEU 4.9 0.2 - - - +
80K VAL* 1.3 89.9 - - + +
82K GLU* 1.3 65.3 + - - +
83K ASP* 3.2 9.3 + - + +
84K ARG* 3.6 25.6 + - + +
85K LEU* 3.3 19.1 + - - +
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Residues in contact with GLU 82 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1485J GLN* 3.1 26.3 + - - +
25K LYS* 5.9 0.3 + - - -
80K VAL 3.3 4.1 + - - -
81K PRO* 1.3 70.2 - - - +
83K ASP* 1.3 66.1 + - - +
85K LEU* 3.3 27.6 - - - +
86K GLN* 3.7 18.7 + - + +
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Residues in contact with ASP 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81K PRO* 3.0 7.5 - - + +
82K GLU* 1.3 82.3 - - - +
84K ARG* 1.3 90.0 + - + +
85K LEU 3.1 0.4 + - - -
86K GLN* 3.5 8.5 + - - +
87K LYS* 3.7 16.1 + - - +
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Residues in contact with ARG 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1495J ILE* 3.7 29.0 - - + +
1498J ALA* 4.9 17.9 + - - +
1499J ARG* 6.1 1.9 - - - +
1502J ALA* 5.2 12.8 - - - +
81K PRO* 3.6 20.6 + - + +
83K ASP* 1.3 88.6 + - + +
85K LEU* 1.3 65.6 + - - +
86K GLN 3.2 0.2 - - - -
87K LYS* 3.1 20.9 + - + -
88K GLU* 3.2 26.6 + - + +
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Residues in contact with LEU 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1485J GLN* 3.6 35.7 - - + +
1486J VAL 5.0 5.8 - - - +
1487J VAL* 3.8 20.9 - - + -
1495J ILE* 3.9 8.7 - - + +
29K GLN* 5.3 9.2 - - - +
80K VAL* 3.8 20.0 - - + -
81K PRO 3.3 14.3 + - - +
82K GLU* 3.3 27.1 - - + +
83K ASP 3.1 0.8 - - - -
84K ARG* 1.3 78.5 - - - +
86K GLN* 1.3 62.1 + - + +
88K GLU* 5.5 0.2 - - - +
89K MET* 3.1 27.8 + - + +
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Residues in contact with GLN 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K ARG* 4.2 17.8 - - - +
82K GLU* 3.7 17.0 + - + +
83K ASP 3.5 7.7 + - - +
84K ARG 3.2 0.2 - - - -
85K LEU* 1.3 83.2 - - + +
87K LYS* 1.3 62.8 + - - +
88K GLU 3.5 0.4 - - - -
89K MET* 3.8 2.7 - - + -
90K GLU* 2.8 45.1 + - - +
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Residues in contact with LYS 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K ASP* 3.7 13.5 + - - +
84K ARG* 3.1 18.2 + - + +
86K GLN* 1.3 80.0 - - - +
88K GLU* 1.3 64.1 + - + +
89K MET 3.3 0.8 + - - -
90K GLU* 4.7 0.5 - - - +
91K ARG* 3.3 21.8 + - - +
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Residues in contact with GLU 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491J THR* 5.0 3.1 - - - +
1494J ALA* 2.9 28.6 - - + +
1495J ILE* 3.3 26.0 - - + +
1498J ALA* 3.2 25.8 - - - +
84K ARG* 3.2 16.4 + - - +
85K LEU 5.5 0.2 - - - +
87K LYS* 1.3 82.2 - - + +
89K MET* 1.3 62.2 + - - +
91K ARG* 3.5 32.0 + - - +
92K LEU* 3.3 29.8 + - - +
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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