Contacts of the strand formed by residues 37 - 42 (chain D) in PDB entry 5LF0
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 ALA 37 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D SER 3.5 1.1 + - - +
36D THR* 1.3 76.0 - - - +
38D ILE* 1.3 64.3 - - - +
49D ALA 3.3 7.4 - - - +
50D VAL* 3.7 19.1 - - + -
77D ALA* 4.4 14.4 - - + -
78D MET 4.4 6.1 - - - +
142D LEU* 4.2 2.2 - - + -
168D ARG 3.9 0.5 - - - +
169D ALA* 3.2 4.9 - - - +
170D ILE* 2.9 53.4 + - + +
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Residues in contact with ILE 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D THR* 4.4 6.7 - - + -
37D ALA* 1.3 79.3 - - - +
39D GLY* 1.3 61.1 + - - +
40D ILE* 4.1 7.2 - - + -
47D CYS* 3.8 0.7 - - - +
48D LEU* 3.3 5.5 - - - +
49D ALA* 2.7 42.5 + - + +
142D LEU* 4.0 4.4 - - - +
168D ARG 3.4 6.3 - - - +
169D ALA* 4.3 12.3 - - + -
177D ALA* 4.7 3.4 - - + -
181D LEU* 4.1 21.1 - - + -
198D SER* 3.6 45.5 - - - +
201D ILE* 3.7 28.5 - - + -
202D LEU* 4.0 15.5 - - + +
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Residues in contact with GLY 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ILE* 1.3 74.3 - - - +
40D ILE* 1.3 64.4 + - - +
47D CYS 3.4 7.9 - - - -
48D LEU* 4.0 10.8 - - - -
142D LEU* 3.8 3.7 - - - +
153D LEU* 3.4 19.7 - - - +
167D ALA* 3.2 3.6 - - - -
168D ARG 2.9 35.4 + - - +
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Residues in contact with ILE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ILE* 4.1 2.2 - - + -
39D GLY* 1.3 79.8 - - - +
41D GLN* 1.3 62.6 + - - +
42D THR* 4.1 6.1 + - + +
46D VAL* 3.2 6.7 - - - +
47D CYS* 3.0 41.6 + - - -
153D LEU* 4.0 1.7 - - - +
166D ASP 3.7 3.4 - - - -
167D ALA* 3.9 11.0 - - + -
181D LEU* 3.9 19.3 - - + -
184D VAL* 5.8 0.7 - - + -
185D TYR* 3.9 26.9 - - + -
189D MET* 4.4 4.3 - - + -
194D ALA* 3.4 45.3 - - + +
197D SER* 4.5 4.9 - - - -
198D SER* 3.8 20.9 - - - +
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Residues in contact with GLN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ILE* 1.3 72.4 - - - +
42D THR* 1.3 66.7 + - - +
45D GLY 4.1 2.0 - - - -
46D VAL* 4.1 3.8 - - + -
151D PRO* 3.4 33.0 + - + +
152D GLN* 3.3 8.2 - - - +
153D LEU* 2.9 32.5 + - + +
164D GLN* 2.8 32.7 + - - +
165D CYS 3.7 1.2 - - - +
166D ASP* 2.9 24.0 + - - +
185D TYR* 2.9 31.6 + - - -
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Residues in contact with THR 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ILE* 4.1 5.6 - - + +
41D GLN* 1.3 83.1 + - - +
43D SER* 1.3 62.7 + - - +
44D GLU 3.1 13.6 + - - -
45D GLY 2.8 30.1 + - - +
151D PRO* 3.2 17.0 - - - +
185D TYR* 4.9 1.6 - - + -
187D LYS 5.2 3.1 - - - -
189D MET* 3.4 22.9 - - + +
190D THR 3.6 10.5 - - - +
191D LEU* 3.7 13.0 + - + -
194D ALA* 3.6 31.2 - - + -
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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