Contacts of the strand formed by residues 39 - 44 (chain P) in PDB entry 4N3E
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 PHE 39 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P LEU* 3.5 36.3 - - + -
32P VAL* 4.0 26.4 - - + +
35P GLN* 3.3 32.0 + - - +
36P PRO* 3.4 18.7 - - - +
38P VAL* 1.3 89.2 - - + +
40P LYS* 1.3 61.8 + - - +
57P ILE* 3.3 30.7 - - + -
58P THR 3.6 5.8 - - - +
59P PHE* 3.7 22.9 - + - -
60P VAL* 3.7 6.8 - - - +
68P MET* 4.1 6.1 - - + -
201P 2AN 3.6 27.8 - + - -
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Residues in contact with LYS 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P VAL* 3.7 13.3 - - - +
39P PHE* 1.3 72.6 - - - +
41P SER* 1.3 63.9 + - - +
58P THR* 2.6 37.8 + - + +
59P PHE 3.6 17.6 + - - +
60P VAL* 4.2 10.8 - - + +
61P ASP* 3.2 32.2 + - - -
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Residues in contact with SER 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P VAL* 3.6 12.1 - - - +
39P PHE 3.9 0.2 - - - -
40P LYS* 1.3 85.9 - - - +
42P GLY* 1.3 59.7 + - - +
43P GLU* 4.6 12.7 + - - +
56P LYS 4.7 1.0 + - - -
57P ILE* 3.4 5.0 - - - +
58P THR* 2.6 57.2 + - - +
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Residues in contact with GLY 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P HIS* 3.6 23.5 + - - +
29P GLN* 4.0 18.0 - - - +
32P VAL* 3.6 6.9 - - - +
41P SER* 1.3 77.4 - - - +
43P GLU* 1.3 74.5 + - - +
56P LYS 3.2 13.0 - - - -
57P ILE* 4.1 3.1 - - - -
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Residues in contact with GLU 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P HIS* 4.4 8.5 + - - +
29P GLN* 5.2 11.5 - - + +
41P SER* 4.6 13.1 + - - +
42P GLY* 1.3 81.4 - - - +
44P ILE* 1.3 73.1 + - + +
45P ILE* 5.0 1.0 - - - +
55P THR* 3.9 1.9 - - - -
56P LYS* 3.1 26.4 + - - +
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Residues in contact with ILE 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P HIS* 4.2 15.7 - - + +
43P GLU* 1.3 87.4 - - + +
45P ILE* 1.3 61.5 + - - +
46P GLU 3.7 5.2 - - - +
47P GLY 4.1 19.5 + - - +
48P ASP 4.1 15.5 - - - +
49P GLY* 5.5 1.6 - - - -
53P THR* 3.1 26.2 - - + -
54P VAL 2.7 25.8 - - - +
55P THR* 4.0 13.2 - - + +
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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