Contacts of the strand formed by residues 47 - 54 (chain D) in PDB entry 5DIR
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 PHE 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D VAL* 3.0 48.5 + - + +
43D ILE* 2.8 46.6 + - + +
46D LEU* 1.3 77.7 - - + +
48D SER* 1.3 79.0 + - - +
49D TRP* 3.5 38.1 - + - -
126D ILE* 3.5 29.6 - - + -
127D LEU 3.6 6.7 - - - -
128D VAL* 4.4 7.4 - - + -
129D HIS* 3.8 1.0 + - - -
203D OLC 5.0 7.6 - - + -
205D OLC 4.1 39.7 - - + -
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Residues in contact with SER 48 (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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39D GLN* 4.6 14.4 + - - -
40D ILE 3.3 14.6 - - - -
41D VAL* 3.5 21.3 - - - +
42D VAL* 4.1 1.6 - - - +
43D ILE 4.8 0.2 + - - -
44D PRO* 5.8 0.3 - - - +
47D PHE* 1.3 86.4 + - - +
49D TRP* 1.3 68.0 + - - +
125D PHE 3.8 0.2 - - - +
127D LEU* 3.0 42.2 + - - +
129D HIS* 4.0 13.6 + - - -
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Residues in contact with TRP 49 (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 PHE* 3.4 39.3 - + + -
34D LEU* 4.2 3.1 - - + -
39D GLN* 3.3 4.7 - - - -
40D ILE* 2.8 52.8 + - + +
42D VAL* 3.3 25.9 - - + +
47D PHE* 3.5 35.2 - + - -
48D SER* 1.3 76.2 - - - +
50D THR* 1.3 61.7 + - - +
125D PHE* 3.3 31.2 - + - -
126D ILE* 4.2 6.7 - - + -
202D OLC 3.6 56.9 + - + -
203D OLC 3.8 27.7 - - + -
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Residues in contact with THR 50 (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 PHE* 4.4 0.9 - - - +
34D LEU* 3.5 12.4 - - - +
37D TYR* 4.0 8.1 - - - -
38D GLN 2.7 20.7 + - - -
39D GLN* 4.0 13.2 + - - +
49D TRP* 1.3 76.9 - - - +
51D LEU* 1.3 72.3 + - - +
52D ALA* 4.9 2.1 - - + +
124D ASP 4.2 4.0 - - - +
125D PHE* 2.8 46.0 + - - +
127D LEU* 3.9 23.3 - - + +
138D ALA* 4.3 12.3 - - + -
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Residues in contact with LEU 51 (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 PHE* 4.0 16.4 - - + +
31D GLN* 4.0 19.1 - - + +
34D LEU* 3.3 31.6 - - + +
35D SER* 3.5 23.3 - - - +
36D MET* 3.6 9.0 - - + +
37D TYR* 2.8 30.7 + - - -
38D GLN 3.6 3.4 + - - -
50D THR* 1.3 85.4 + - - +
52D ALA* 1.3 61.0 + - - +
53D TYR* 4.4 20.4 - - + +
123D VAL* 3.8 28.7 - - + -
124D ASP 3.5 1.1 - - - +
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Residues in contact with ALA 52 (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 MET* 4.6 4.7 - - - -
37D TYR* 5.2 11.4 - - + -
50D THR* 5.0 3.6 - - + +
51D LEU* 1.3 77.0 - - - +
53D TYR* 1.3 72.2 + - - +
54D ASN* 3.9 0.4 - - + -
122D VAL 3.6 1.4 - - - +
123D VAL* 3.6 0.5 - - - +
124D ASP* 2.9 48.8 + - + +
138D ALA* 4.6 11.2 - - + -
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Residues in contact with TYR 53 (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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31D GLN* 3.3 35.2 + - - +
36D MET* 3.8 41.9 - - + +
51D LEU* 4.4 24.6 - - + +
52D ALA* 1.3 80.5 - - - +
54D ASN* 1.3 61.0 + - - +
55D THR* 3.7 7.7 + - - +
121D HIS* 3.3 47.1 - + + +
122D VAL 3.6 1.8 - - - -
123D VAL* 4.1 7.4 - - + -
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Residues in contact with ASN 54 (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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52D ALA* 3.9 0.6 + - + -
53D TYR* 1.3 70.0 - - - +
55D THR* 1.3 59.5 + - - +
56D GLY* 2.7 35.7 + - - -
116D ARG* 5.9 0.2 + - - -
121D HIS* 3.7 4.5 - - - +
122D VAL* 2.9 37.0 + - + +
124D ASP* 3.2 26.8 + - - +
137D PRO* 5.9 1.4 - - - +
138D ALA 4.7 2.2 + - - -
203G SER* 3.1 31.1 + - - +
204G ALO 3.5 15.6 + - - -
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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