Contacts of the strand formed by residues 88 - 95 (chain M) in PDB entry 2ZJR
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 VAL 88 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M ARG* 3.8 11.6 + - - +
34M ARG* 2.7 68.2 - - - +
36M ASP* 4.4 2.2 - - - -
81M PHE* 3.4 14.4 - - + -
82M PRO 4.6 0.4 - - - +
83M PHE 4.4 8.1 - - - +
85M SER* 2.6 32.2 + - - +
86M PRO* 3.1 5.2 - - - +
87M LEU* 1.3 75.0 - - + +
89M ASN* 1.3 70.6 + - - +
90M GLN* 4.3 0.9 - - - +
91M VAL* 4.2 3.6 - - + -
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Residues in contact with ASN 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M ARG* 2.5 31.8 + - - -
35M VAL* 3.5 17.4 + - + +
36M ASP* 4.9 1.8 - - - -
37M THR* 3.7 23.0 + - - +
86M PRO 5.1 3.9 - - - +
87M LEU 3.6 3.8 + - - -
88M VAL* 1.3 72.3 - - - +
90M GLN* 1.3 79.8 + - - +
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Residues in contact with GLN 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M ARG* 4.4 5.6 - - - +
33M VAL 4.8 0.2 - - - -
34M ARG* 3.9 2.4 + - - -
35M VAL* 3.2 38.9 + - + +
88M VAL* 3.7 1.1 - - - -
89M ASN* 1.3 112.8 + - + +
91M VAL* 1.3 67.7 - - - +
92M THR* 4.9 9.4 - - + -
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Residues in contact with VAL 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M LEU* 4.0 12.4 - - + +
25M PRO* 3.2 29.6 - - + +
27M PHE* 4.0 21.5 - - + -
32M THR* 3.1 33.2 - - + -
33M VAL 3.7 4.7 - - - +
34M ARG* 2.6 50.7 - - + +
66M PHE* 4.3 4.3 - - + -
90M GLN* 1.3 73.6 - - - +
92M THR* 1.3 65.2 + - - +
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Residues in contact with THR 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M PRO* 4.8 2.0 - - - -
32M THR* 3.2 4.6 - - - +
33M VAL* 3.1 41.8 + - + +
35M VAL* 4.9 8.7 - - + -
90M GLN* 4.9 8.7 - - + -
91M VAL* 1.3 83.3 - - - +
93M ILE* 1.3 75.0 + - - +
94M VAL* 4.7 4.9 - - - +
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Residues in contact with ILE 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M PRO* 3.6 28.7 - - + -
26M ASP* 4.5 3.6 - - - +
27M PHE* 3.5 43.1 - - + +
29M PRO 5.4 2.0 - - - +
31M ASP 3.7 12.1 - - - +
32M THR* 4.5 1.3 - - + +
92M THR* 1.3 87.6 + - - +
94M VAL* 1.3 63.0 + - - +
95M GLU* 3.7 9.4 - - - +
96M ARG* 4.1 24.2 - - + +
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Residues in contact with VAL 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M ASP* 2.9 29.9 + - + +
32M THR 4.2 1.6 - - - -
33M VAL* 3.2 35.0 - - + -
51M GLU* 3.8 11.9 - - - +
92M THR* 4.3 3.1 - - - +
93M ILE* 1.3 76.9 - - - +
95M GLU* 1.3 74.2 + - + +
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Residues in contact with GLU 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M GLY* 3.2 1.6 - - - -
31M ASP* 3.1 51.2 + - - +
93M ILE* 3.7 5.1 - - - +
94M VAL* 1.3 88.4 - - + +
96M ARG* 1.3 71.1 + - - +
97M GLY* 4.3 0.2 - - - -
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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