Contacts of the strand formed by residues 44 - 49 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L ARG* 3.6 1.0 - - - +
41L CYS* 3.1 26.4 + - - +
42L LYS 3.5 3.0 + - - -
43L ASP* 1.3 79.5 - - - +
45L VAL* 1.3 69.4 + - - +
140L TYR* 4.0 3.4 - - - -
146L ALA* 3.4 14.6 - - - +
186L CYS* 3.4 9.0 - - - -
216L VAL 3.1 11.4 - - - -
217L GLY* 3.6 3.1 - - - -
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Residues in contact with VAL 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L ILE 3.4 19.1 - - - +
40L ARG* 4.3 5.4 - - + -
41L CYS 4.6 0.4 - - - +
44L GLY* 1.3 80.0 - - - +
46L VAL* 1.3 71.0 + - - +
47L PHE* 4.3 13.7 - - + -
138L GLY* 4.6 2.0 - - - -
139L SER 3.9 12.8 - - - +
146L ALA* 4.2 0.7 - - + -
147L GLN 3.5 31.2 - - - +
148L LEU* 3.9 28.3 - - + -
186L CYS* 3.9 1.2 - - - -
214L SER 3.7 0.2 - - - +
215L TRP* 3.6 1.0 - - - -
216L VAL* 2.5 50.6 + - + +
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Residues in contact with VAL 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L GLY* 3.1 22.2 - - - -
39L ILE* 2.9 15.5 + - - +
41L CYS* 5.2 0.4 - - + -
45L VAL* 1.3 81.4 - - - +
47L PHE* 1.3 73.2 + - - +
186L CYS* 4.2 10.3 - - - +
189L ILE* 3.9 30.1 - - + -
190L VAL* 4.2 20.2 - - + -
193L VAL* 3.9 19.7 - - + -
213L LEU* 5.2 0.9 - - + -
214L SER 3.3 11.9 - - - +
215L TRP* 4.1 21.3 - - + -
227L VAL* 5.5 0.4 - - + -
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Residues in contact with PHE 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L ILE 3.3 4.5 - - - +
38L GLY* 3.5 16.6 - - - -
45L VAL* 4.3 9.4 - - + -
46L VAL* 1.3 82.1 - - - +
48L GLY* 1.3 59.3 + - - +
66L LEU* 3.6 14.8 - - + -
74L GLY 3.9 20.6 - - - -
75L MET 5.3 0.2 - - - -
76L ALA* 3.6 17.5 - - + -
136L MET* 3.8 18.4 - - + -
137L LEU 3.9 2.5 - - - -
138L GLY* 3.6 29.2 - - - -
148L LEU* 3.5 28.9 - - + -
193L VAL* 4.7 0.4 - - - -
213L LEU* 3.4 7.9 - - - +
214L SER* 2.9 51.3 + - - -
216L VAL* 5.6 0.7 - - + -
224L HIS* 4.1 13.2 - + - -
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Residues in contact with GLY 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L ALA* 3.4 0.7 - - - -
37L ILE* 2.8 36.8 + - - +
47L PHE* 1.3 73.8 - - - +
49L VAL* 1.3 66.8 + - - +
66L LEU* 4.7 0.2 - - - -
193L VAL* 4.0 13.5 - - - +
197L ILE* 3.9 9.4 - - - +
212L GLU 3.3 10.5 - - - -
213L LEU* 3.7 10.5 - - - -
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Residues in contact with VAL 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L THR 3.9 3.4 - - - +
36L ALA* 3.8 15.5 - - + -
48L GLY* 1.3 79.1 - - - +
50L GLU* 1.3 55.1 + - - +
51L LYS* 2.7 24.9 + - + +
65L ARG* 3.6 49.6 - - + +
66L LEU* 3.5 35.7 - - + -
76L ALA* 5.2 1.1 - - + -
77L VAL 5.5 0.2 - - - +
197L ILE* 4.2 1.9 - - - +
211L LEU* 3.5 11.2 - - - +
212L GLU* 3.1 32.0 + - + -
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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