Contacts of the strand formed by residues 35 - 40 (chain C) in PDB entry 4NY0
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 ARG 35 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C GLU* 1.3 73.7 - - - +
36C VAL* 1.3 74.6 + - + +
57C ARG* 3.2 7.0 - - - +
58C HIS* 2.9 45.4 + - + -
60C ASP* 5.5 0.6 + - - -
105C SER* 3.8 34.8 + - - +
108C ARG* 3.4 45.1 - - - +
109C GLU* 5.3 2.4 - - - +
112C GLU* 3.8 18.2 + - - -
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU 5.6 0.4 - - - +
35C ARG* 1.3 83.6 - - + +
37C LEU* 1.3 56.3 + - - +
55C ILE* 4.2 22.2 - - + -
56C ILE 3.3 7.2 - - - +
57C ARG* 4.2 15.3 - - + -
58C HIS* 4.3 0.9 - - - -
108C ARG* 2.5 37.9 + - - +
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C VAL* 1.3 77.4 - - - +
38C LYS* 1.3 65.1 + - - +
39C VAL* 3.7 26.3 + - + +
54C SER 3.5 1.9 - - - +
55C ILE* 3.4 4.2 - - - -
56C ILE* 2.8 37.9 + - + +
58C HIS* 4.0 8.1 - - + -
67C ILE* 4.5 14.8 - - + -
85C LEU* 5.0 4.5 - - + -
104C VAL* 3.9 22.2 - - + -
108C ARG* 3.8 24.2 - - - +
122C TYR* 3.8 47.8 - - + -
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 1.3 76.4 - - - +
39C VAL* 1.3 61.8 + - - +
40C PHE* 3.9 36.9 + - + -
53C ALA* 4.3 19.1 - - + -
54C SER 3.4 3.4 - - - +
55C ILE* 3.7 29.4 - - + -
108C ARG* 5.4 0.8 - - - +
122C TYR* 3.8 20.1 + - - +
403C GLU* 4.6 9.9 + - - -
404C GLU 5.9 1.8 - - - -
405C ASP 5.5 2.8 + - - -
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 3.7 31.2 - - + +
38C LYS* 1.3 74.9 - - - +
40C PHE* 1.3 72.4 - - - +
41C HIS* 3.8 3.9 + - + -
53C ALA* 3.4 1.8 - - - -
54C SER* 2.9 35.2 + - - +
56C ILE* 4.9 2.9 - - + -
67C ILE* 3.9 9.2 - - + -
71C ILE* 3.7 32.8 - - + -
85C LEU* 4.0 13.0 - - + -
122C TYR* 3.5 7.9 - - + +
124C LEU* 3.7 20.4 - - + +
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Residues in contact with PHE 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LYS* 3.9 45.5 - - + -
39C VAL* 1.3 75.3 - - - +
41C HIS* 1.3 60.6 + - - +
42C TYR* 5.7 0.2 - - - -
50C THR* 3.9 23.8 - - - -
51C THR* 5.7 0.9 - - - -
52C TRP 3.7 12.1 - - - +
53C ALA* 4.0 4.9 - - + -
120C TRP 5.9 0.4 - - - -
121C LYS* 3.7 46.7 - - + -
122C TYR 2.8 20.3 + - - +
123C GLU* 3.3 8.5 - - + +
124C LEU 2.8 25.6 + - - -
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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