Contacts of the strand formed by residues 39 - 44 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31T LEU* 3.5 38.6 - - + -
32T VAL* 3.9 25.8 - - + +
35T GLN* 3.2 30.2 + - - +
36T PRO* 3.8 21.1 - - - +
38T VAL* 1.3 92.5 - - + +
40T LYS* 1.3 62.2 + - - +
57T ILE* 3.1 30.5 - - + -
58T THR 3.6 5.2 - - - +
59T PHE* 3.4 32.5 - + - -
60T VAL* 3.9 5.0 - - - +
68T MET* 3.6 14.1 - - + -
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Residues in contact with LYS 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32T VAL* 4.3 9.0 - - - +
39T PHE* 1.3 74.7 - - - +
41T SER* 1.3 60.6 + - - +
58T THR* 2.7 26.4 + - + +
59T PHE 3.5 17.9 - - - +
60T VAL* 3.8 15.4 - - + +
61T ASP* 3.8 27.5 + - - +
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Residues in contact with SER 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32T VAL* 3.5 13.9 - - - +
39T PHE 3.6 0.8 - - - -
40T LYS* 1.3 87.1 - - - +
42T GLY* 1.3 60.2 + - - +
43T GLU* 4.4 14.7 + - - -
56T LYS* 4.9 1.6 + - - -
57T ILE* 3.3 2.9 - - - +
58T THR* 2.8 39.7 + - - +
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Residues in contact with GLY 42 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28T HIS* 3.6 27.4 - - - -
29T GLN* 4.4 15.4 - - - +
32T VAL* 3.3 8.3 - - - +
41T SER* 1.3 75.4 - - - +
43T GLU* 1.3 61.8 + - - +
56T LYS 3.0 9.4 - - - -
57T ILE* 4.0 4.3 - - - -
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Residues in contact with GLU 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28T HIS* 4.1 8.1 - - - +
29T GLN* 6.1 0.2 - - - -
41T SER* 4.4 12.7 + - - +
42T GLY* 1.3 75.7 - - - +
44T ILE* 1.3 65.6 + - - +
45T ILE* 3.8 21.0 - - + +
55T THR* 3.2 7.8 - - - -
56T LYS* 2.7 72.3 + - + +
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Residues in contact with ILE 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T GLU* 5.4 4.7 - - - +
28T HIS* 3.8 26.4 - - + +
29T GLN* 6.0 1.8 - - - +
43T GLU* 1.3 78.5 - - - +
45T ILE* 1.3 65.0 + - - +
46T GLU 3.9 7.0 - - - +
47T GLY 4.1 13.9 - - - +
48T ASP 5.2 2.0 - - - +
49T GLY* 4.5 13.0 - - - +
53T THR* 3.1 36.1 - - + -
54T VAL 3.6 6.3 - - - +
55T THR* 4.3 3.1 - - + +
72T PHE* 6.5 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