Contacts of the strand formed by residues 81 - 89 (chain T) in PDB entry 5HJD
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 PHE 81 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17H ARG* 3.1 14.5 + - - +
18H KCR 4.1 25.4 - - + +
19H GLN 6.2 0.2 - - - -
32T TRP* 3.8 36.8 - + - -
55T LEU* 4.0 2.7 - - + -
56T HIS* 3.6 37.7 - + + -
59T PHE* 4.0 13.5 - + - -
79T ALA 3.7 13.7 - - - -
80T GLY* 1.3 78.8 - - - +
82T ILE* 1.3 73.5 + - - +
83T LEU* 3.7 27.1 - - + -
104T LEU* 3.0 40.5 + - + +
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Residues in contact with ILE 82 (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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17H ARG* 4.4 4.5 - - - +
54T HIS 4.6 0.5 - - - +
55T LEU 6.0 0.2 - - - -
81T PHE* 1.3 82.6 - - - +
83T LEU* 1.3 61.2 + - - +
84T PRO* 3.2 14.6 - - + +
101T ASP* 4.0 34.1 - - + +
102T TYR 3.4 2.7 - - - +
103T ASP* 3.8 35.7 - - + +
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Residues in contact with LEU 83 (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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32T TRP* 4.4 0.2 - - + -
34T VAL* 3.9 14.4 - - + -
53T PHE* 3.8 13.7 - - + -
54T HIS 3.4 37.2 - - - +
55T LEU* 3.6 22.2 - - + +
81T PHE* 3.6 15.0 + - + -
82T ILE* 1.3 72.8 - - - +
84T PRO* 1.3 69.1 - - - +
85T ILE* 3.2 12.7 + - + +
102T TYR* 2.6 43.3 + - + +
104T LEU* 3.6 32.5 - - + -
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Residues in contact with PRO 84 (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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54T HIS* 3.0 61.0 + - + +
82T ILE* 3.2 16.6 - - + +
83T LEU* 1.3 80.5 - - - +
85T ILE* 1.3 61.2 + - - +
99T ARG* 3.7 28.0 - - - +
100T PHE 3.5 7.4 - - - +
101T ASP* 4.0 11.0 - - - +
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Residues in contact with ILE 85 (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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13T LEU* 3.9 22.4 - - + -
34T VAL* 4.4 8.3 - - + -
36T VAL* 3.9 13.9 - - + -
51T VAL* 3.7 27.4 - - + -
52T VAL 3.5 4.9 - - - +
53T PHE* 4.0 28.0 - - + -
83T LEU* 3.4 15.5 - - + +
84T PRO* 1.3 73.0 - - - +
86T GLU* 1.3 65.7 + - - +
87T VAL* 4.3 5.1 + - + -
98T VAL 3.8 0.9 - - - +
99T ARG* 3.4 5.0 - - - +
100T PHE* 2.8 39.6 + - + +
102T TYR* 3.7 25.8 - - + -
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Residues in contact with GLU 86 (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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50T LYS 4.0 0.7 - - - +
51T VAL* 3.3 4.5 - - - +
52T VAL* 2.7 47.4 + - + +
54T HIS* 3.2 26.0 + - + +
84T PRO 4.2 0.2 + - - -
85T ILE* 1.3 76.0 - - - +
87T VAL* 1.3 62.6 + - - +
88T TYR* 3.3 29.8 + - + -
97T LYS* 3.1 34.1 + - + -
98T VAL 3.5 3.8 - - - +
99T ARG* 4.0 28.3 - - + -
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Residues in contact with VAL 87 (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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11T LEU* 4.4 18.4 - - + -
36T VAL* 4.5 10.3 - - + -
44T ILE* 6.2 0.2 - - + -
48T VAL* 3.8 35.2 - - + -
50T LYS 3.7 2.0 - - - -
51T VAL* 4.3 15.7 - - + +
85T ILE* 4.6 7.0 - - + -
86T GLU* 1.3 77.1 - - - +
88T TYR* 1.3 65.9 + - - +
89T PHE* 4.1 14.1 + - + -
97T LYS* 3.1 5.2 - - - -
98T VAL* 2.9 48.4 + - + +
100T PHE* 4.4 9.0 - - + -
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Residues in contact with TYR 88 (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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48T VAL* 3.3 8.7 - - - +
49T GLU* 2.6 40.6 + - + +
50T LYS* 2.8 57.5 + - + +
52T VAL* 4.0 13.6 - - + +
63T LYS* 5.8 1.6 + - - -
86T GLU* 3.3 40.7 + - + -
87T VAL* 1.3 78.7 - - - +
89T PHE* 1.3 57.7 + - - +
96T ARG* 3.7 11.4 - - + -
97T LYS* 3.9 29.8 + - + +
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Residues in contact with PHE 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47T PHE* 3.1 24.2 - + - +
49T GLU* 4.0 14.5 - - - +
87T VAL* 4.1 16.6 - - + -
88T TYR* 1.3 78.8 - - - +
90T LYS* 1.3 54.2 + - - +
91T ASN* 2.7 23.8 + - + +
95T PRO* 3.6 19.7 - - + -
96T ARG* 3.0 28.5 + - - +
97T LYS* 3.7 20.6 - - - -
98T VAL* 3.6 26.2 - - + -
122T LEU* 3.7 18.4 - - + -
124T PHE* 3.5 36.3 - + - -
131T PHE* 3.7 14.4 - - + -
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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