Contacts of the strand formed by residues 46 - 51 (chain C) in PDB entry 3SDI
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 VAL 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C VAL 3.4 17.9 - - - +
41C LYS* 3.6 10.3 - - + +
42C GLY 4.4 0.2 - - - +
45C CYS* 1.3 80.2 - - - +
47C VAL* 1.3 72.4 + - - +
48C LEU* 4.9 0.2 - - + -
139C ALA* 3.7 23.6 - - + -
140C GLY 4.8 2.7 - - - +
141C PHE* 4.9 4.7 - - + -
146C PRO* 3.5 20.9 - - + -
147C LYS 3.8 17.5 - - - +
148C LEU* 4.4 11.4 - - + -
214C VAL* 4.5 0.5 - - - +
215C VAL* 3.0 45.6 + - + +
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Residues in contact with VAL 47 (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 VAL 4.1 0.2 - - - +
39C GLY* 3.2 5.7 - - - -
40C VAL 2.9 32.0 + - - +
45C CYS* 4.3 7.0 - - - -
46C VAL* 1.3 77.5 - - - +
48C LEU* 1.3 66.0 + - - +
49C GLY 4.2 0.4 - - - -
186C VAL 4.8 0.2 - - - +
189C CYS* 3.7 26.2 - - + -
190C VAL* 3.9 24.5 - - + +
193C THR* 3.6 29.3 + - + +
212C ILE* 3.6 29.6 - - + -
213C THR 3.6 5.4 - - - +
214C VAL* 4.5 7.0 - - + -
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Residues in contact with LEU 48 (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 VAL 3.6 3.4 - - - +
39C GLY* 3.9 15.5 - - - -
46C VAL* 4.3 0.9 - - + -
47C VAL* 1.3 82.7 - - - +
49C GLY* 1.3 59.7 + - - +
67C VAL* 3.9 30.3 - - + +
75C VAL* 4.2 17.7 - - + +
77C SER* 3.5 38.8 - - - +
137C LEU* 4.4 11.0 - - + +
139C ALA* 4.3 22.7 - - + -
148C LEU* 4.3 6.7 - - + -
211C GLU 3.8 0.7 - - - +
212C ILE* 3.5 2.6 - - - -
213C THR* 2.9 36.6 + - - +
215C VAL* 5.3 2.9 - - + -
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Residues in contact with GLY 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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37C ALA* 3.4 2.1 - - - -
38C VAL* 2.7 51.3 + - - +
47C VAL 4.2 0.6 - - - -
48C LEU* 1.3 74.5 - - - +
50C CYS* 1.3 65.6 + - - -
193C THR* 4.2 2.9 - - - +
197C LEU* 4.1 8.1 - - - -
211C GLU 3.3 8.3 - - - -
212C ILE* 3.7 13.5 - - - -
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Residues in contact with CYS 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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36C CYS 3.4 8.5 - - - +
37C ALA* 4.1 14.8 - - + -
49C GLY* 1.3 81.4 - - - -
51C GLU* 1.3 63.7 + - - +
66C LYS* 3.9 36.3 - - + +
67C VAL* 4.2 13.7 - - - -
77C SER* 4.1 18.4 - - - -
197C LEU* 4.3 6.7 - - - +
210C ILE* 3.7 6.2 - - - +
211C GLU* 3.1 39.4 + - + +
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Residues in contact with GLU 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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35C THR* 3.4 20.9 + - - +
36C CYS* 3.0 51.3 + - + +
50C CYS* 1.3 77.8 - - - +
52C ARG* 1.3 66.7 + - - +
66C LYS* 4.9 5.2 - - - +
167C ARG* 3.0 46.2 + - - +
197C LEU* 4.5 2.6 - - + +
200C VAL* 4.3 9.1 - - - +
201C VAL* 3.7 35.7 - - + +
209C ASN* 3.6 5.2 - - - +
211C GLU* 6.1 0.4 - - - -
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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