Contacts of the helix formed by residues 101 - 107 (chain J) 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 HIS 101 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1095I LEU* 3.0 34.4 + - + +
1096I ALA* 5.1 4.7 - - + -
1097I LEU* 5.9 1.3 - - + -
99J ALA 4.3 0.2 + - - -
100J ALA* 1.3 70.9 - - - +
102J ILE* 1.3 63.9 + - - +
103J TRP* 3.1 46.6 + + + +
104J PHE* 3.4 36.2 + + + +
105J VAL* 3.4 12.9 + - - +
112J ILE* 5.1 0.2 - - - +
511J TRP 5.8 0.4 - - - +
512J MET* 3.0 14.3 + - - +
514J LEU* 4.7 13.4 - - + +
578J VAL* 5.4 1.1 - - - -
582J ILE* 3.3 46.9 - - + +
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Residues in contact with ILE 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J ALA 3.3 3.6 + - - -
101J HIS* 1.3 71.8 - - - +
103J TRP* 1.3 68.1 + - + +
104J PHE 3.4 0.2 - - - -
105J VAL* 3.7 10.8 - - + -
106J LYS* 2.9 32.9 + - + +
128J TYR* 4.0 11.2 - - - +
579J ASP* 3.2 39.6 + - + +
582J ILE* 3.8 16.9 - - + +
583J ASP* 3.7 32.1 - - + +
586J ARG* 3.7 28.0 - - + +
587J ARG* 4.3 13.9 - - + +
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Residues in contact with TRP 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095I LEU* 3.5 19.3 - - + -
1097I LEU* 4.1 15.9 - - + -
101J HIS* 3.1 25.9 + + - +
102J ILE* 1.3 81.0 - - - +
104J PHE* 1.3 59.3 + + + +
106J LYS* 5.5 0.4 - - - +
107J ASP* 2.8 39.7 + - - +
582J ILE* 4.3 4.0 - - + -
583J ASP* 3.6 18.1 + - + -
586J ARG* 5.8 4.0 - - + -
604J THR* 2.9 47.3 + - + +
607J LEU* 4.4 6.3 - - + -
1443J THR* 6.2 0.4 - - + -
1444J THR* 3.9 27.2 - - - -
1447J LEU* 3.5 43.5 - - + -
1448J THR* 3.9 24.9 - - + -
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Residues in contact with PHE 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095I LEU 6.0 0.2 - - - -
1097I LEU* 5.7 5.4 - - + -
12J LEU* 3.7 21.5 - - + -
101J HIS* 3.5 45.3 - + + +
102J ILE 3.4 0.2 - - - -
103J TRP* 1.3 78.4 - + + +
105J VAL* 1.3 51.9 + - - +
107J ASP* 4.5 4.5 - - - -
110J SER* 2.7 29.1 + - - -
111J LYS* 3.3 18.7 + - + +
112J ILE* 3.4 8.7 - - + +
512J MET* 3.5 48.5 - - + -
1448J THR* 3.9 22.4 - - + -
1451J ALA* 5.7 0.2 - - + -
1452J ILE* 3.5 30.3 - - + -
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Residues in contact with VAL 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J ALA* 4.3 9.0 - - + -
101J HIS 3.4 18.2 - - - +
102J ILE* 3.5 15.7 - - + +
103J TRP 3.1 0.4 - - - -
104J PHE* 1.3 77.6 - - - +
106J LYS* 1.3 72.5 + - + +
107J ASP 4.2 0.2 - - - +
110J SER* 3.2 20.1 + - - -
112J ILE* 3.6 20.4 - - + -
120J ALA* 4.7 11.4 - - + +
123J LEU* 5.1 6.8 - - + +
124J GLU* 5.6 6.1 - - + +
127J LEU* 3.7 27.1 - - + -
128J TYR* 4.9 14.8 - - + -
575J GLN* 5.5 2.9 - - - +
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Residues in contact with LYS 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J ILE* 2.9 22.6 + - + +
103J TRP* 3.7 0.7 - - - -
105J VAL* 1.3 85.2 - - + +
107J ASP* 1.3 61.5 + - - +
108J VAL* 3.6 1.2 + - - -
120J ALA* 5.3 10.2 + - + +
124J GLU* 3.7 28.9 + - - +
128J TYR* 5.9 0.2 - - - +
586J ARG* 2.6 62.3 + - + +
587J ARG* 4.0 20.0 - - + +
7S G 4.5 19.6 + - - +
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Residues in contact with ASP 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J TRP 2.8 21.2 + - - +
104J PHE* 4.3 9.4 - - - +
105J VAL 3.4 1.7 - - - +
106J LYS* 1.3 80.7 - - - +
108J VAL* 1.3 75.0 + - - +
109J PRO* 3.3 22.2 - - + +
110J SER* 3.2 18.4 + - - -
111J LYS* 4.1 9.3 - - - +
586J ARG* 3.9 6.6 + - - +
1444J THR* 4.9 0.8 + - - +
1445J HIS* 3.1 29.9 + - - +
1448J THR* 3.8 24.6 + - + +
1449J GLU* 4.6 0.9 - - - +
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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