Contacts of the strand formed by residues 48 - 52 (chain C) in PDB entry 1I2M
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 HIS 48 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C VAL* 3.7 33.9 - - + +
28C LYS* 6.1 1.3 - - + -
31C LEU* 3.8 24.9 - - + -
45C VAL* 6.2 1.6 - - + -
46C GLU* 3.3 50.4 + - + +
47C VAL* 1.3 73.3 - - - +
49C PRO* 1.3 67.2 - - - +
50C LEU* 3.1 10.4 + - - +
61C PHE 3.3 0.5 - - - +
63C VAL* 2.6 34.7 + - + +
64C TRP* 4.7 3.2 - - - -
65C ASP* 5.2 7.8 + - + -
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Residues in contact with PRO 49 (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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30C HIS 4.6 1.0 - - - +
31C LEU* 3.8 16.0 - - + +
38C LYS* 4.5 8.3 - - + +
47C VAL* 3.4 15.2 - - + +
48C HIS* 1.3 79.9 - - - +
50C LEU* 1.3 60.3 + - - +
51C VAL* 3.9 6.1 + - + +
60C LYS* 3.8 28.9 - - + +
61C PHE 3.5 6.3 - - - +
62C ASN* 3.8 11.4 - - - +
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Residues in contact with LEU 50 (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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27C VAL* 4.0 16.8 - - + +
30C HIS* 3.1 39.0 - - + +
31C LEU* 3.4 24.5 - - + -
48C HIS 3.4 11.2 - - - +
49C PRO* 1.3 70.5 - - - +
51C VAL* 1.3 61.6 + - - +
52C PHE* 3.5 21.2 - - + -
60C LYS* 3.5 0.4 - - - +
61C PHE* 2.7 37.9 + - + +
63C VAL* 3.6 17.0 - - + -
161C PHE* 3.5 36.3 - - + -
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Residues in contact with VAL 51 (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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8C GLN* 5.7 6.1 - - - +
30C HIS 4.8 3.2 + - - +
49C PRO* 3.9 6.2 + - + +
50C LEU* 1.3 71.8 - - - +
52C PHE* 1.3 69.5 + - - +
53C HIS* 4.3 26.1 + - + +
58C PRO* 4.4 10.8 - - + -
59C ILE 3.7 9.2 - - - +
60C LYS* 3.7 33.0 - - + -
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Residues in contact with PHE 52 (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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30C HIS* 3.6 33.4 - + + -
50C LEU* 3.5 32.5 - - + -
51C VAL* 1.3 78.3 - - - +
53C HIS* 1.3 62.9 - - - +
54C THR* 3.7 2.9 + - + +
58C PRO* 3.4 1.2 - - - +
59C ILE* 2.8 42.1 + - + +
61C PHE* 3.8 23.6 - + + -
158C GLU* 4.8 5.4 - - + -
161C PHE* 3.5 24.2 - + + -
176C PHE* 3.4 50.3 - + + -
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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