Contacts of the strand formed by residues 69 - 74 (chain D) in PDB entry 5A0Q
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D LEU* 3.2 11.4 + - + -
66D ASP* 3.0 47.6 + - - +
68D ASN* 1.3 97.6 + - - +
70D CYS* 1.3 63.7 + - - +
102D VAL 3.9 4.7 - - - +
104D VAL* 3.9 22.4 - - + -
107D ILE* 4.0 22.4 - - + -
133D ILE* 3.8 22.0 - - + -
134D VAL 3.6 11.9 - - - +
135D GLY* 4.2 0.9 - - - -
211D MET* 5.0 0.5 - - - +
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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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41D VAL* 4.8 1.1 - - - -
43D LEU* 4.1 1.8 - - - -
63D CYS 3.4 14.8 - - - +
64D ALA* 4.0 4.7 - - + +
65D LEU* 3.8 7.0 - - - -
69D VAL* 1.3 74.7 - - - +
71D MET* 1.4 62.7 + - - +
133D ILE* 3.7 5.7 - - - +
134D VAL* 2.8 60.3 + - - +
135D GLY 4.3 0.4 - - - -
211D MET* 3.6 22.7 - - - -
217D LEU* 3.4 29.8 - - + -
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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* 4.7 5.2 - - - +
63D CYS* 2.9 33.2 + - + +
65D LEU* 3.5 13.5 - - + -
70D CYS* 1.4 75.9 - - - +
72D ALA* 1.4 62.1 + - - +
73D PHE* 3.8 27.5 - - + +
80D ALA 4.0 5.6 - - - +
83D VAL* 4.4 7.4 - - + -
84D ILE* 3.8 34.3 - - + -
111D ILE* 4.2 11.2 - - + -
129D ILE* 4.0 19.7 - - + -
131D ALA* 3.8 29.6 - - + -
132D LEU 3.8 4.9 - - - +
133D ILE* 4.0 15.5 - - + +
217D LEU* 5.3 0.7 - - - +
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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* 3.8 5.2 - - + +
33D VAL 5.2 0.9 - - - +
43D LEU* 4.0 28.5 - - + -
44D GLY 5.1 1.6 - - - +
45D VAL* 4.4 17.9 - - + -
63D CYS 5.2 0.2 - - - +
71D MET* 1.4 73.8 - - - +
73D PHE* 1.3 66.0 + - - +
132D LEU* 3.0 45.2 + - + +
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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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32D ALA* 4.3 4.7 - - - +
45D VAL* 4.6 6.9 - - - +
63D CYS* 3.7 30.7 - - + -
71D MET* 4.0 28.4 - - + +
72D ALA* 1.3 78.4 - - - +
74D ALA* 1.3 66.6 - - - +
75D GLY 5.3 0.7 - - - -
77D THR* 3.3 35.4 - - - -
80D ALA* 3.3 37.0 - - + -
81D ARG* 4.7 5.4 - - + -
84D ILE* 5.4 0.2 - - + -
129D ILE* 4.4 3.6 - - + -
131D ALA* 3.9 15.3 - - + +
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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* 4.1 8.3 - - + -
30D SER 3.6 15.9 - - - +
32D ALA* 3.9 6.3 - - + -
72D ALA 3.8 0.4 + - - -
73D PHE* 1.3 77.1 - - - +
75D GLY* 1.3 60.7 + - - +
129D ILE* 3.4 6.2 - - - +
130D SER 3.0 36.2 + - - +
161D ILE* 3.4 32.1 - - + +
162D GLY* 4.5 1.6 - - - +
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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