Contacts of the strand formed by residues 44 - 49 (chain I) in PDB entry 5DSV
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 GLY 44 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I ARG* 3.6 0.9 - - - +
41I CYS* 3.1 26.2 + - - +
42I LYS 3.5 2.8 + - - -
43I ASP* 1.3 80.9 - - - +
45I VAL* 1.3 69.9 + - - +
140I TYR* 4.0 3.6 - - - -
146I ALA* 3.5 14.2 - - - +
186I CYS* 3.4 9.2 - - - -
216I VAL 3.1 12.1 - - - -
217I GLY* 3.6 2.7 - - - -
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Residues in contact with VAL 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I ILE 3.4 19.7 - - - +
40I ARG* 4.3 5.2 - - + -
41I CYS 4.6 0.4 - - - +
44I GLY* 1.3 80.6 - - - +
46I VAL* 1.3 70.3 + - - +
47I PHE* 4.2 14.6 - - + -
138I GLY* 4.5 1.8 - - - -
139I SER 3.9 12.8 - - - +
146I ALA* 4.2 0.7 - - + -
147I GLN 3.4 31.0 - - - +
148I LEU* 3.9 27.4 - - + -
186I CYS* 3.8 0.8 - - - -
215I TRP* 3.7 1.6 - - - -
216I VAL* 2.5 51.2 + - + +
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Residues in contact with VAL 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I GLY* 3.1 22.3 - - - -
39I ILE* 2.9 15.8 + - - +
41I CYS* 5.2 0.4 - - + -
45I VAL* 1.3 82.4 - - - +
47I PHE* 1.3 73.4 + - - +
186I CYS* 4.2 9.6 - - - +
189I ILE* 3.9 30.3 - - + -
190I VAL* 4.2 20.6 - - + -
193I VAL* 3.9 19.3 - - + -
213I LEU* 5.2 0.9 - - + -
214I SER 3.2 12.1 - - - +
215I TRP* 4.1 22.0 - - + -
227I VAL* 5.5 0.4 - - + -
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Residues in contact with PHE 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ILE 3.3 3.6 - - - +
38I GLY* 3.6 15.5 - - - -
45I VAL* 4.2 9.9 - - + -
46I VAL* 1.3 81.0 - - - +
48I GLY* 1.3 58.4 + - - +
66I LEU* 3.5 14.8 - - + -
74I GLY* 3.9 15.3 - - - -
75I MET 5.2 0.2 - - - -
76I ALA* 3.5 18.4 - - + -
136I MET* 3.8 18.2 - - + -
137I LEU 3.9 2.7 - - - -
138I GLY* 3.5 35.7 - - - -
148I LEU* 3.5 28.3 - - + -
193I VAL* 4.7 0.7 - - - -
213I LEU* 3.4 7.6 - - - +
214I SER* 2.9 51.1 + - - -
216I VAL* 5.6 0.4 - - + -
224I HIS* 4.1 12.6 - + - -
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Residues in contact with GLY 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I ALA* 3.4 0.5 - - - -
37I ILE 2.8 37.4 + - - +
47I PHE* 1.3 73.7 - - - +
49I VAL* 1.3 67.1 + - - +
66I LEU* 4.7 0.2 - - - -
193I VAL* 4.0 12.2 - - - +
197I ILE* 3.9 10.3 - - - +
212I GLU 3.3 10.8 - - - -
213I LEU* 3.7 11.0 - - - -
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Residues in contact with VAL 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I THR 3.9 3.1 - - - +
36I ALA* 3.8 15.5 - - + -
48I GLY* 1.3 79.9 - - - +
50I GLU* 1.3 55.9 + - - +
51I LYS* 2.7 24.7 + - + +
65I ARG* 3.6 48.0 - - + +
66I LEU* 3.5 36.3 - - + -
76I ALA* 5.2 0.2 - - + -
197I ILE* 4.1 2.1 - - - +
211I LEU* 3.5 10.5 - - - +
212I GLU* 3.1 31.9 + - + -
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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