Contacts of the strand formed by residues 108 - 115 (chain H) in PDB entry 6XXD
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 GLY 108 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D ILE* 4.2 21.3 - - - -
22D PRO 5.4 0.6 + - - -
24D LEU* 6.2 1.6 - - - -
70G LYS* 5.5 1.1 - - - -
44H VAL* 5.6 2.5 - - - -
103H ALA* 3.5 0.3 - - - -
104H THR 2.9 35.6 + - - -
105H PRO 3.9 4.7 + - - -
106H ASP 3.5 2.2 - - - -
107H LYS* 1.3 82.3 - - - +
109H VAL* 1.3 61.0 + - - -
110H TYR* 3.4 10.2 - - - -
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Residues in contact with VAL 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ALA* 4.7 8.9 + - + +
18D ALA* 4.6 17.7 - - - +
21D ILE* 4.9 8.5 - - + +
37H THR* 4.3 25.0 - - + +
40H LEU* 3.8 38.1 - - + +
41H ASN* 4.0 11.0 - - + +
44H VAL* 3.9 27.1 - - + -
101H PHE* 4.8 4.5 - - + -
102H ALA 3.6 11.9 - - - +
103H ALA* 4.1 2.9 - - + -
107H LYS 4.0 1.9 + - - +
108H GLY* 1.3 70.7 - - - -
110H TYR* 1.3 64.8 + - - +
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Residues in contact with TYR 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H PHE* 3.4 9.9 - - - +
102H ALA* 2.8 52.2 + - + +
104H THR* 4.2 9.1 - - + +
107H LYS* 3.5 53.4 - - + +
108H GLY 3.4 15.7 - - - -
109H VAL* 1.3 75.2 - - - +
111H LYS* 1.3 69.1 + - - +
112H THR* 5.2 0.7 - - - -
124H CYS* 3.7 6.8 - - - +
125H PRO* 2.7 50.8 + - + +
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Residues in contact with LYS 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ARG* 5.2 2.6 - - - +
98H THR* 5.7 0.9 - - - +
99H VAL* 4.0 23.8 - - + +
100H TRP 3.7 4.3 - - - +
101H PHE* 3.7 27.1 - - + -
110H TYR* 1.3 86.6 - - - +
112H THR* 1.3 59.6 + - - +
113H ASN* 5.1 1.2 - - - +
52J ILE* 3.7 28.2 + - - +
53J ASP* 3.9 24.5 + - - +
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Residues in contact with THR 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H ILE* 6.0 1.8 - - + -
99H VAL* 3.4 23.6 - - - +
100H TRP* 3.0 41.1 + - + +
101H PHE* 5.2 0.7 - - - -
102H ALA* 5.3 4.9 - - + +
110H TYR* 4.2 3.3 + - - -
111H LYS* 1.3 74.3 - - - +
113H ASN* 1.3 75.0 + - - +
114H THR* 3.8 20.6 + - - +
121H PRO* 4.2 8.4 - - + +
125H PRO* 3.6 34.2 - - + +
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Residues in contact with ASN 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H VAL* 4.2 6.1 - - - +
111H LYS 5.1 1.4 - - - +
112H THR* 1.3 82.7 + - - +
114H THR* 1.3 61.7 + - - +
115H ALA* 3.5 2.9 + - - +
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Residues in contact with THR 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H VAL* 3.3 7.0 - - - +
100H TRP* 3.2 28.7 + - + -
112H THR* 3.3 9.4 + - - +
113H ASN* 1.3 76.7 - - - +
115H ALA* 1.3 66.8 + - - +
118H SER* 4.2 8.7 - - - -
119H SER 3.5 25.6 - - - +
121H PRO* 3.8 25.2 - - + +
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Residues in contact with ALA 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H THR 4.0 11.9 - - - +
99H VAL* 4.2 3.4 - - + -
100H TRP* 2.9 16.5 + - - -
113H ASN 3.5 3.5 + - - +
114H THR* 1.3 76.5 - - - +
116H VAL* 1.3 64.2 + - - +
117H THR* 3.3 18.2 - - + +
118H SER* 3.2 24.0 + - - +
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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