Contacts of the strand formed by residues 73 - 78 (chain X) in PDB entry 1XDM
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 ILE 73 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X LYS* 3.9 1.8 - - - -
28X GLY 3.5 3.6 - - - +
30X LEU* 3.7 9.9 - - + +
69X ILE* 3.0 34.4 + - + +
70X ASN* 4.2 3.3 - - - -
72X SER* 1.3 81.1 - - - +
74X GLY* 1.3 57.5 + - - +
75X GLY 3.2 24.7 - - - +
76X VAL* 3.6 20.4 - - + -
102X ILE* 3.4 27.7 - - + +
299X PHE* 3.9 13.9 - - + -
305X LEU* 3.7 30.1 - - + -
327X PHE* 4.4 7.9 - - + -
331X ALA* 4.3 10.5 - - + -
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Residues in contact with GLY 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X SER 3.8 4.4 - - - +
22X ILE* 3.7 24.4 - - - -
27X LYS* 3.2 31.9 - - - +
28X GLY 3.0 8.3 + - - -
73X ILE* 1.3 72.5 - - - +
75X GLY* 1.3 55.3 + - - +
101X GLY 4.8 5.3 - - - +
102X ILE* 4.4 1.4 - - - -
103X VAL* 3.5 24.1 + - - +
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Residues in contact with GLY 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X ILE* 4.2 8.3 - - - -
28X GLY 3.4 4.1 + - - -
29X ILE* 3.0 31.9 - - - +
30X LEU 3.0 2.8 + - - -
73X ILE* 3.2 4.8 + - - +
74X GLY* 1.3 81.9 - - - +
76X VAL* 1.3 63.7 + - - -
102X ILE* 4.2 0.4 - - - +
103X VAL* 3.3 21.3 - - - +
144X PHE* 4.3 2.2 - - - -
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Residues in contact with VAL 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X LEU* 3.8 21.8 - - + +
32X ALA* 4.3 1.6 - - + -
63X PHE* 3.9 30.1 - - + -
73X ILE* 3.6 18.2 - - + -
75X GLY* 1.3 76.2 - - - -
77X ILE* 1.3 71.0 + - - +
78X LEU* 3.8 3.9 + - + -
97X LEU* 4.6 8.5 - - + -
102X ILE* 3.5 30.3 - - + -
103X VAL 2.7 11.4 + - - +
104X VAL* 3.4 3.6 - - - +
105X GLY 2.6 31.5 + - - +
144X PHE* 4.1 1.5 - - - -
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Residues in contact with ILE 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X ILE* 3.8 15.0 - - + -
30X LEU 2.9 13.2 + - - +
31X ALA* 4.7 1.3 - - - -
32X ALA* 3.2 24.1 + - - +
33X ASP* 2.9 39.7 - - + +
75X GLY 4.3 0.2 - - - -
76X VAL* 1.3 77.9 - - - +
78X LEU* 1.3 65.8 + - - +
105X GLY 3.5 7.9 - - - +
106X ILE 4.9 0.2 - - - +
107X LYS* 4.4 9.0 - - + +
144X PHE* 3.3 22.0 - - + -
146X LYS* 4.3 13.9 - - + -
185X ILE* 3.7 23.8 - - + -
229X LYS* 4.0 20.9 - - - +
300X SER* 4.1 0.2 - - - +
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Residues in contact with LEU 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X ALA* 3.8 7.9 - - + +
33X ASP* 3.7 5.9 - - - +
63X PHE* 3.6 26.5 - - + -
76X VAL* 4.7 3.6 - - + -
77X ILE* 1.3 76.4 - - - +
79X PHE* 1.3 62.9 + - - +
82X THR* 3.3 34.3 - - + +
83X LEU* 4.3 21.1 - - + +
93X PHE* 5.4 2.5 - - + +
94X ARG* 5.3 5.2 - - - -
97X LEU* 4.2 15.5 - - + -
104X VAL* 3.4 28.5 - - + -
105X GLY 2.5 15.6 + - - +
106X ILE* 3.7 2.2 - - + +
107X LYS* 3.1 28.6 + - - +
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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