Contacts of the strand formed by residues 38 - 43 (chain D) in PDB entry 5L5H
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 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D ILE 3.4 17.9 - - - +
33D ALA* 3.9 12.8 - - + -
37D GLY* 1.3 77.0 - - - +
39D VAL* 1.3 70.0 + - - +
40D LEU* 4.1 2.1 + - + +
137D ALA* 3.5 21.7 - - + +
138D GLY 4.1 5.4 - - - +
145D TYR* 3.8 22.0 - - + -
146D GLN 3.7 19.5 - - - +
147D LEU* 4.2 9.4 - - + -
185D LEU* 4.6 0.2 - - - +
213D CYS* 3.2 4.6 - - - +
214D ILE* 3.0 44.6 + - + +
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Residues in contact with VAL 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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30D ILE 4.0 0.2 - - - +
31D GLY* 3.3 5.0 - - - -
32D ILE* 2.8 34.6 + - + +
37D GLY 5.3 0.2 - - - +
38D VAL* 1.3 73.0 - - - +
40D LEU* 1.3 66.7 + - - +
185D LEU* 3.7 27.8 - - + -
188D ALA* 3.8 22.9 - - + -
189D GLU* 4.1 20.4 - - + +
192D VAL* 3.9 25.6 - - + +
211D LEU* 4.1 17.5 - - + -
212D SER 3.5 11.7 - - - +
213D CYS* 4.6 3.1 - - + -
223D TYR* 5.7 0.7 - - + +
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Residues in contact with LEU 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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30D ILE 3.6 3.6 - - - +
31D GLY* 3.9 5.6 - - - -
38D VAL* 4.1 2.2 + - + +
39D VAL* 1.3 86.2 - - - +
41D GLY* 1.3 56.6 + - - +
59D ILE* 3.7 4.7 - - + +
67D GLY* 4.2 2.7 - - - -
68D CYS 3.8 15.5 - - - +
69D ALA* 3.6 40.2 - - + +
135D LEU* 3.8 10.5 - - + +
137D ALA* 3.4 30.7 - - + -
147D LEU* 3.9 17.5 - - + -
211D LEU* 3.5 1.6 - - - +
212D SER* 2.7 59.6 + - - +
213D CYS* 5.7 0.7 - - - -
220D PHE* 5.0 3.6 - - + -
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Residues in contact with GLY 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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29D ALA* 4.0 0.2 - - - +
30D ILE* 2.8 39.7 + - - +
40D LEU* 1.3 74.3 - - - +
42D VAL* 1.3 67.1 + - - +
59D ILE* 4.2 0.7 - - - -
69D ALA* 5.2 0.5 - - - +
192D VAL* 3.8 19.5 - - - +
196D LEU* 4.2 7.7 - - - +
210D GLN 3.3 10.8 - - - -
211D LEU* 4.1 2.7 - - - -
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Residues in contact with VAL 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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27D SER* 5.8 0.2 - - - +
28D THR 3.5 5.8 - - - +
29D ALA* 3.8 18.4 - - + -
41D GLY* 1.3 78.7 - - - +
43D GLU* 1.3 66.6 + - - +
44D LYS* 4.9 4.7 - - + +
58D LYS* 4.0 24.7 - - + +
59D ILE* 3.6 35.0 - - + -
69D ALA* 3.9 9.6 - - + -
70D MET 4.6 1.8 - - - +
196D LEU* 4.1 9.2 - - - +
209D ALA* 3.5 6.8 - - - +
210D GLN* 3.0 42.7 + - + +
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Residues in contact with GLU 43 (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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27D SER* 3.1 21.4 + - - -
28D THR* 2.8 45.9 + - - +
42D VAL* 1.3 72.6 - - - +
44D LYS* 1.3 62.1 + - - +
45D ARG* 3.2 49.6 + - + +
58D LYS* 3.8 6.4 - - - +
196D LEU* 4.0 3.9 - - + +
200D MET* 3.7 46.2 - - + +
201D GLU* 4.6 7.4 + - - +
202D GLU* 5.2 4.7 - - - +
208D ASN 4.0 3.1 - - - -
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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