Contacts of the strand formed by residues 102 - 108 (chain T) in PDB entry 3ALQ
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 TRP 102 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81T ASP* 3.5 33.0 - - + -
98T CYS* 4.0 15.1 - - + +
99T ARG* 3.1 54.5 + - + +
100T PRO 3.4 13.7 + - - -
101T GLY* 1.3 91.0 + - - +
103T TYR* 1.3 60.5 + - - +
115T CYS* 3.9 12.8 - - + -
116T ALA* 3.1 34.3 - - - +
117T PRO* 3.6 34.0 - - + +
118T LEU* 4.2 6.5 - - - +
132T THR 5.1 0.3 - - - +
133T GLU* 3.6 20.1 - - - +
151W THR* 4.2 18.4 - - + -
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Residues in contact with TYR 103 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR* 5.7 4.7 - - - +
73A HIS* 3.4 24.4 + + - -
98T CYS* 3.6 6.0 - - - -
102T TRP* 1.3 74.7 - - - +
104T CYS* 1.3 67.6 + - - +
105T ALA* 3.6 19.9 - - + +
115T CYS* 3.6 2.8 - - - -
116T ALA* 2.8 60.5 + - + +
117T PRO 4.3 4.5 - - - -
118T LEU* 4.0 8.1 - - + -
132T THR 3.5 23.1 - - - +
133T GLU 4.3 4.5 - - - -
134T THR 4.8 1.1 - - - -
135T SER* 3.7 11.7 - - - +
136T ASP* 3.4 54.1 + - + +
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Residues in contact with CYS 104 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98T CYS* 3.9 3.6 - - - -
103T TYR* 1.3 82.6 - - - +
105T ALA* 1.3 64.5 + - - +
106T LEU* 3.1 25.1 + - - -
107T SER* 4.0 10.8 + - - -
111T GLY 4.6 0.4 - - - -
112T CYS* 2.0 54.1 - - + -
133T GLU* 3.3 21.3 + - + +
134T THR* 4.0 18.1 - - + +
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Residues in contact with ALA 105 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A HIS* 4.3 12.3 - - + +
75A LEU* 4.9 5.2 - - + +
103T TYR* 3.5 27.8 + - + +
104T CYS* 1.3 72.9 - - - +
106T LEU* 1.3 63.7 + - - +
114T LEU* 2.9 30.5 + - + +
116T ALA* 4.2 13.9 - - + -
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Residues in contact with LEU 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.6 34.1 - - + -
77A THR* 4.2 18.2 - - + +
97A ILE* 4.1 26.7 - - + -
137A ASN* 5.0 10.1 - - + +
115C TYR* 4.7 4.5 - - - +
104T CYS* 3.1 16.4 - - - -
105T ALA* 1.3 82.2 - - - +
107T SER* 1.3 73.6 + - - +
113T ARG* 3.1 31.0 + - + +
114T LEU* 3.4 18.6 + - + +
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Residues in contact with SER 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104T CYS* 4.1 11.6 + - - +
106T LEU* 1.3 85.6 - - - +
108T LYS* 1.3 68.8 + - - +
111T GLY 3.7 8.0 + - - -
113T ARG* 4.9 1.2 - - - -
134T THR* 4.5 15.6 - - - +
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Residues in contact with LYS 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ALA* 3.9 26.0 + - - +
146C GLU* 3.0 35.9 - - + +
75T GLY* 5.8 1.8 - - - -
76T SER* 5.4 5.3 + - - -
82T GLN* 5.7 1.2 + - - -
93T ASN* 5.7 7.2 - - - +
94T ARG 5.9 2.2 - - - +
96T CYS* 4.7 14.9 - - - +
106T LEU 3.6 3.0 + - - -
107T SER* 1.3 81.7 - - - +
109T GLN* 1.3 71.6 + - + +
110T GLU* 3.1 12.8 + - - +
111T GLY 2.8 25.2 + - - +
112T CYS 3.7 19.4 + - - -
113T ARG* 3.8 26.5 - - + +
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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