Contacts of the strand formed by residues 96 - 101 (chain A) in PDB entry 2NMU
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 MSE 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ILE* 3.5 39.9 - - + -
88A ALA* 4.0 18.4 - - + -
89A VAL 3.1 9.6 - - - +
90A SER* 3.7 17.0 - - - -
94A GLY 3.5 8.0 + - - +
95A VAL* 1.3 81.5 - - - +
97A LEU* 1.3 72.1 + - - +
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.5 7.2 - - + +
56A TYR* 4.2 18.4 - - + +
65A LEU* 3.6 30.1 - - + -
69A PHE* 4.7 15.0 - - + -
87A LEU 4.1 0.2 - - - +
88A ALA* 3.4 3.5 - - - +
89A VAL* 2.9 39.1 + - + +
91A ASP* 6.1 1.1 - - + +
95A VAL* 5.3 8.3 - - + +
96A MSE 1.3 82.3 - - - +
98A GLY* 1.3 59.6 + - - +
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Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.1 8.4 - - - +
56A TYR* 3.5 18.3 - - - -
87A LEU 3.2 11.9 - - - -
88A ALA* 4.2 4.9 - - - -
97A LEU* 1.3 76.6 - - - +
99A GLY* 1.3 57.7 + - - -
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.8 7.9 - - - +
55A ARG 3.9 7.6 - - - -
56A TYR* 4.6 6.3 - - - -
57A ALA 5.4 1.8 - - - -
86A HIS* 3.4 11.5 - - - +
87A LEU 3.0 31.0 + - - +
98A GLY* 1.3 75.4 - - - -
100A HIS* 1.3 61.9 + - - -
101A MSE 3.4 0.2 + - - -
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Residues in contact with HIS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.4 2.6 - - - -
55A ARG* 2.8 87.1 + - + +
83A GLU 5.4 1.6 - - - -
84A HIS* 3.4 35.8 + + - -
85A LEU 3.6 18.4 + - - -
86A HIS* 3.7 13.8 + - + +
99A GLY* 1.3 69.2 - - - -
101A MSE 1.3 70.2 + - - +
102A MSE 3.8 21.1 - - - +
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Residues in contact with MSE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.1 21.5 - - + -
25A PHE* 3.2 37.4 - - + -
49A LEU* 4.5 3.8 - - + -
53A ALA 3.9 3.6 - - - -
54A LEU* 4.2 3.8 - - - -
71A VAL* 6.1 0.2 - - + -
74A LEU* 3.5 31.2 - - + -
85A LEU* 2.9 26.3 + - - +
87A LEU* 3.5 33.0 - - + -
99A GLY 3.4 3.8 + - - -
100A HIS* 1.3 80.2 + - - +
102A MSE 1.3 70.8 + - - +
105A CYS* 3.3 38.1 - - + -
111A LEU* 6.0 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