Contacts of the strand formed by residues 69 - 74 (chain D) in PDB entry 5LN3
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 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D LEU* 3.6 28.6 + - + -
66D ASP* 2.8 30.2 - - + +
68D ASN* 1.3 90.5 - - - +
70D CYS* 1.3 71.9 + - - +
102D VAL 6.0 0.9 - - - +
104D VAL* 4.3 11.0 - - + -
107D ILE* 4.3 24.7 - - + -
133D ILE* 5.1 9.2 - - + -
134D VAL 3.5 11.0 - - - +
135D GLY* 4.1 5.8 - - - -
136D PHE 3.9 14.6 - - - +
137D ASP* 5.1 2.0 - - - +
211D MET* 3.7 2.2 - - - +
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Residues in contact with CYS 70 (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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43D LEU* 4.4 5.2 - - + -
62D ILE* 3.8 30.5 - - + -
63D CYS 3.2 17.9 - - - +
64D ALA* 4.3 6.7 - - - -
65D LEU* 5.0 0.9 - - - +
66D ASP 5.4 0.7 - - - -
69D VAL* 1.3 83.4 - - - +
71D MET* 1.4 61.5 + - - +
133D ILE* 3.9 2.6 - - - +
134D VAL* 2.9 32.9 + - - +
211D MET* 3.6 23.1 - - + +
217D LEU* 4.4 19.7 - - - -
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Residues in contact with MET 71 (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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43D LEU* 5.1 1.3 - - - -
61D LYS 3.1 4.2 - - - +
62D ILE* 3.7 1.1 - - - -
63D CYS* 2.8 41.7 + - + +
65D LEU* 4.1 20.6 - - + -
70D CYS* 1.4 74.9 - - - +
72D ALA* 1.4 64.3 + - - +
73D PHE* 4.5 18.8 - - + -
80D ALA* 4.6 3.4 - - - +
83D VAL* 4.1 33.9 - - + -
84D ILE* 4.5 16.8 - - + -
87D ALA* 6.1 1.3 - - - -
111D ILE* 4.8 5.6 - - + -
129D ILE* 4.9 8.1 - - + -
131D ALA* 4.3 13.9 - - + -
132D LEU 3.5 5.2 - - - -
133D ILE* 3.7 27.8 - - + -
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Residues in contact with ALA 72 (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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32D ALA* 4.9 8.3 - - + -
43D LEU* 4.2 30.2 - - + +
45D VAL* 4.9 4.5 - - + -
61D LYS* 3.4 18.6 - - + +
62D ILE* 4.9 1.6 - - - -
71D MET* 1.4 72.2 - - - +
73D PHE* 1.4 62.7 + - - +
131D ALA* 3.3 8.1 - - - +
132D LEU* 2.9 42.3 + - + +
161D ILE* 6.0 0.2 - - - -
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Residues in contact with PHE 73 (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 SER* 5.4 1.0 - - - -
32D ALA* 5.1 6.7 - - - +
60D ARG 4.5 1.6 - - - -
61D LYS* 3.4 78.9 + - + +
63D CYS* 3.9 18.2 - - - -
71D MET* 4.5 17.5 - - + -
72D ALA* 1.4 76.9 - - - +
74D ALA* 1.3 70.4 + - - +
75D GLY* 5.1 0.2 - - - -
76D LEU 3.6 23.6 - - - -
77D THR* 4.1 9.6 - - + -
80D ALA* 3.9 24.9 - - + -
84D ILE* 5.5 0.2 - - + -
129D ILE* 5.2 7.0 - - + -
130D SER 3.7 10.1 - - - +
131D ALA* 4.1 2.2 - - + +
161D ILE* 5.1 5.6 - - - +
439I TYR 3.9 12.1 - - - -
440I LEU 4.0 7.2 - - - -
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Residues in contact with ALA 74 (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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26D VAL* 4.3 29.5 - - + +
29D GLY* 4.8 1.3 - - - -
30D SER* 4.6 23.6 - - - +
61D LYS* 4.5 3.6 - - - +
73D PHE* 1.3 80.5 - - - +
75D GLY* 1.4 58.3 + - - +
129D ILE* 3.7 8.4 - - - +
130D SER 3.0 31.4 + - - +
161D ILE* 4.7 10.5 - - + -
162D GLY* 5.6 0.9 - - - -
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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