Contacts of the strand formed by residues 46 - 52 (chain D) in PDB entry 3AP4
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 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D VAL* 4.1 10.1 - - + -
45D ARG* 1.3 75.2 - - - +
47D GLN* 1.3 78.3 + - - +
48D VAL* 4.2 17.7 - - + -
67D ASN* 2.6 28.5 + - - -
68D PRO* 3.2 42.4 + - + +
70D PHE* 3.9 22.2 - + - -
97D PHE* 4.1 17.7 - + - -
103D PHE* 4.1 12.1 - + - -
105D ILE* 4.4 7.0 - - + -
140D ILE* 4.9 2.7 - - + -
141D TYR 3.3 16.4 - - - +
142D GLY* 4.2 1.3 - - - -
143D LYS 4.0 6.1 - - - +
144D VAL* 3.6 42.6 - - + -
146D ILE* 5.5 1.6 - - + -
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Residues in contact with GLN 47 (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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45D ARG* 2.7 30.0 + - - +
46D PHE* 1.3 77.9 - - - +
48D VAL* 1.3 62.7 + - - +
49D ASP* 2.8 30.8 + - - +
59D ARG* 4.0 12.5 - - - +
65D HIS* 3.4 28.3 - - + -
66D PHE 3.2 11.7 - - - +
67D ASN* 3.9 1.8 - - - +
140D ILE* 3.3 10.4 - - - +
141D TYR* 3.0 58.4 + - + +
142D GLY* 5.9 0.5 - - - -
2H GAL 5.2 1.4 + - - -
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Residues in contact with VAL 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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35D ILE* 3.7 28.0 - - + -
46D PHE* 4.2 18.2 - - + -
47D GLN* 1.3 74.0 - - - +
49D ASP* 1.3 60.8 + - - +
50D LEU* 4.5 5.5 - - + +
64D PHE* 3.4 4.2 - - + +
66D PHE* 2.9 51.0 + - + +
105D ILE* 4.6 5.4 - - + -
107D ILE* 4.2 15.9 - - + -
138D LEU* 3.6 28.3 - - + -
139D GLY 3.4 4.0 - - - -
140D ILE* 4.5 9.0 - - + -
146D ILE* 6.2 0.2 - - + -
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Residues in contact with ASP 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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47D GLN* 2.8 32.4 + - - +
48D VAL* 1.3 80.5 - - - +
50D LEU* 1.3 63.0 + - - +
51D GLN* 3.7 18.8 + - + +
59D ARG* 4.1 8.8 + - - -
62D VAL* 3.8 15.2 - - + +
64D PHE 3.4 2.5 - - - -
65D HIS* 2.8 28.1 + - - -
137D THR 3.8 0.2 - - - +
138D LEU* 3.6 6.2 - - - +
139D GLY 2.7 37.1 + - - +
141D TYR* 3.5 11.6 - - + -
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Residues in contact with LEU 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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23D ILE* 4.7 8.5 - - + -
27D LEU* 4.5 2.9 - - + -
33D ILE* 4.3 24.5 - - + -
48D VAL* 4.5 8.3 - - + -
49D ASP* 1.3 77.9 - - - +
51D GLN* 1.3 55.7 + - - +
62D VAL 3.5 1.9 - - - -
63D ALA* 2.8 32.7 + - - +
64D PHE* 3.0 32.0 + - + +
107D ILE* 4.7 6.1 - - + -
114D PHE* 3.4 39.3 - - + -
135D ILE* 3.6 22.9 - - + -
137D THR 3.5 2.9 - - - -
138D LEU* 3.9 20.0 - - + -
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Residues in contact with GLN 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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20D VAL* 5.0 1.8 - - - +
49D ASP* 3.7 19.1 - - + +
50D LEU* 1.3 79.0 - - - +
52D ASN* 1.3 60.3 + - - +
53D GLY 3.0 23.0 + - - +
54D SER* 4.0 9.3 - - - +
59D ARG* 5.9 0.2 + - - -
60D ALA* 4.2 7.5 - - + +
61D ASP 3.4 12.3 - - - +
62D VAL* 4.3 9.1 - - + +
63D ALA 5.3 0.2 - - - -
135D ILE* 3.4 7.0 - - - +
136D ASP 3.0 23.6 + - - -
137D THR* 2.8 37.4 + - - +
139D GLY* 4.0 4.4 - - - -
141D TYR* 2.8 37.5 + - - -
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Residues in contact with ASN 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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51D GLN* 1.3 68.6 - - - +
53D GLY* 1.3 65.0 + - - +
60D ALA* 3.5 16.0 - - - +
61D ASP* 3.1 29.9 + - + +
63D ALA* 5.2 2.7 - - + +
130D ILE* 5.8 4.9 - - + +
134D LYS* 3.3 46.0 + - + +
135D ILE* 4.6 0.4 - - - +
136D ASP* 4.5 5.0 - - - +
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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