Contacts of the strand formed by residues 97 - 104 (chain Q) 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 LYS 97 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86Q GLU* 3.4 23.0 + - + +
87Q VAL 3.3 15.3 - - - +
88Q TYR* 3.4 47.8 + - + +
89Q PHE* 3.7 7.2 - - - -
95Q PRO* 3.3 15.8 - - - +
96Q ARG* 1.3 85.8 - - + +
98Q VAL* 1.3 66.1 + - - +
99Q ARG* 6.2 1.8 - - + -
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Residues in contact with VAL 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85Q ILE 3.7 1.0 - - - +
86Q GLU* 3.4 3.7 - - - +
87Q VAL* 3.0 37.8 + - + -
89Q PHE* 3.6 24.5 - - + -
95Q PRO* 6.4 0.4 - - + -
97Q LYS* 1.3 77.2 - - - +
99Q ARG* 1.3 67.7 + - - +
100Q PHE* 3.6 36.8 - - + -
122Q LEU* 4.1 18.4 - - + -
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Residues in contact with ARG 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Q PRO* 4.2 17.9 - - + +
85Q ILE 3.3 11.4 - - - +
86Q GLU* 4.3 22.2 - - + +
97Q LYS* 6.2 1.8 - - + -
98Q VAL* 1.3 80.0 - - - +
100Q PHE* 1.3 75.0 + - - +
101Q ASP* 2.9 36.2 + - - +
201Q SO4 4.4 5.4 + - - -
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Residues in contact with PHE 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Q LEU* 4.5 12.6 - - + -
13Q LEU* 3.9 28.0 - - + -
84Q PRO* 3.5 0.2 - - - +
85Q ILE* 2.6 50.4 + - + +
87Q VAL* 4.5 7.6 - - + -
98Q VAL* 3.6 30.3 - - + -
99Q ARG* 1.3 78.1 - - - +
101Q ASP* 1.3 59.7 + - - +
102Q TYR* 3.3 5.0 + - - +
118Q ARG* 3.6 26.5 - - - +
120Q GLU* 3.6 34.1 - - + -
122Q LEU* 3.8 28.3 - - + -
201Q SO4 3.5 5.8 - - - -
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Residues in contact with ASP 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Q ILE* 4.0 20.6 - - + +
83Q LEU 4.0 3.8 - - - -
84Q PRO* 3.7 11.2 - - - +
99Q ARG* 2.9 43.2 + - - -
100Q PHE* 1.3 65.5 - - - +
102Q TYR* 1.3 62.6 + - - +
103Q ASP* 3.7 1.6 + - - +
118Q ARG* 3.4 13.6 + - - -
201Q SO4 2.4 36.2 + - - +
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Residues in contact with TYR 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Q LEU* 4.7 8.5 - - + -
14Q GLY* 3.5 10.1 - - - -
15Q HIS* 2.4 61.5 + + + -
34Q VAL* 3.8 21.1 - - + -
82Q ILE* 3.5 2.5 - - - -
83Q LEU* 2.5 52.5 + - + +
85Q ILE* 3.7 18.8 - - + -
100Q PHE* 3.3 3.4 + - + +
101Q ASP* 1.3 71.6 - - - +
103Q ASP* 1.3 74.7 + - + +
104Q LEU* 3.2 12.4 + - + -
116Q HIS* 3.4 24.5 - + - -
118Q ARG* 4.0 31.6 - - + +
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Residues in contact with ASP 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I ARG* 2.3 41.3 + - - -
15Q HIS* 3.8 5.9 - - - -
82Q ILE* 4.0 16.8 - - + +
101Q ASP 3.7 3.6 + - - +
102Q TYR* 1.3 82.6 - - + +
104Q LEU* 1.3 57.8 + - - +
105Q PHE* 3.2 27.7 + - + +
116Q HIS* 5.4 0.3 - - - -
118Q ARG* 4.7 2.5 - - - +
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Residues in contact with LEU 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I ARG* 3.7 0.3 + - - -
15Q HIS* 3.8 20.0 - - + -
32Q TRP* 3.6 45.3 - - + -
34Q VAL* 3.9 13.5 - - + -
80Q GLY* 3.3 5.4 - - - -
81Q PHE* 2.9 51.7 + - + +
83Q LEU* 3.6 30.5 - - + -
102Q TYR* 3.2 10.6 + - + -
103Q ASP* 1.3 70.3 - - - +
105Q PHE* 1.3 56.0 + - - +
106Q LEU* 3.7 25.8 - - + -
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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