Contacts of the strand formed by residues 6 - 13 (chain D) in PDB entry 3SAJ
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 ASN 6 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ASN* 4.5 0.2 + - - -
302A ALA* 3.2 29.7 + - - +
303A GLY* 4.0 0.3 - - - -
304A ASP* 3.3 32.6 + - - +
4D PRO* 3.9 14.9 - - - +
5D ASN* 1.3 91.1 - - - +
7D ILE* 1.3 67.2 + - - +
8D GLN* 3.5 27.5 + - - +
36D LYS* 3.3 18.3 - - - +
38D LEU* 4.6 7.2 - - + -
65D TYR* 4.4 1.6 - - - -
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Residues in contact with ILE 7 (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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3D MET* 4.3 9.0 - - + -
4D PRO* 4.0 18.8 - - + -
6D ASN* 1.3 77.1 - - - +
8D GLN* 1.3 61.9 + - - +
9D ILE* 3.4 15.7 + - + +
35D PRO* 3.3 29.8 - - + -
36D LYS 2.7 10.3 + - - +
37D LEU* 3.4 19.0 - - + -
38D LEU* 3.0 19.5 + - - -
65D TYR* 3.7 48.7 - - + -
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Residues in contact with GLN 8 (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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304A ASP* 4.5 9.5 + - - -
6D ASN* 3.5 29.9 + - - +
7D ILE* 1.3 73.9 - - - +
9D ILE* 1.3 62.9 + - - +
38D LEU* 3.4 14.8 - - + +
40D GLN* 3.7 34.1 - - - +
62D LYS 5.9 2.2 - - - +
63D GLY 4.6 4.0 - - - +
64D VAL* 4.2 13.9 - - + +
65D TYR* 3.1 40.6 + - + -
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Residues in contact with ILE 9 (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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7D ILE* 3.6 25.6 - - + +
8D GLN* 1.3 83.9 - - - +
10D GLY* 1.3 74.4 + - - +
24D PHE* 5.0 9.4 - - + -
37D LEU* 4.2 25.6 - - + -
38D LEU 3.0 10.2 + - - +
39D PRO* 3.5 7.1 - - + +
40D GLN* 2.9 27.4 + - - -
41D ILE* 4.7 0.7 - - - +
64D VAL* 4.1 2.5 - - - -
65D TYR* 4.6 0.2 - - + -
66D ALA* 3.6 29.6 - - + +
68D PHE* 4.4 15.3 - - + +
91D ILE* 6.3 0.7 - - + -
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Residues in contact with GLY 10 (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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9D ILE* 1.3 82.4 - - - +
11D GLY* 1.3 54.1 + - - -
24D PHE* 5.4 0.3 - - - -
40D GLN 3.7 8.3 - - - -
41D ILE* 4.2 1.4 - - - +
59D GLN* 3.3 17.3 - - - -
64D VAL* 3.5 15.7 - - - +
66D ALA 2.8 14.6 + - - -
67D ILE* 3.9 2.5 - - - -
68D PHE* 2.7 29.4 + - - +
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Residues in contact with GLY 11 (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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10D GLY* 1.3 73.9 - - - -
12D LEU* 1.3 63.6 + - - +
13D PHE* 3.9 4.0 - - - -
40D GLN 3.6 3.2 + - - -
41D ILE* 3.0 28.6 - - - +
42D ASP 3.1 13.9 + - - +
59D GLN* 2.9 21.5 + - - -
67D ILE* 4.5 0.2 - - - -
68D PHE* 2.9 9.6 - - - -
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Residues in contact with LEU 12 (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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11D GLY* 1.3 79.7 - - - +
13D PHE* 1.3 62.8 + - - +
42D ASP 3.8 2.2 - - - +
44D VAL* 4.0 15.9 - - + -
46D ILE* 4.3 1.2 - - - +
52D MET* 3.5 27.6 - - + +
55D ARG* 3.4 36.6 - - + -
56D PHE* 4.5 17.5 - - + +
59D GLN* 3.8 9.6 - - - +
67D ILE* 3.8 23.1 - - + -
68D PHE 2.9 8.5 + - - -
69D GLY* 3.2 8.2 - - - -
70D PHE* 3.0 29.7 + - - +
79D LEU* 5.1 1.6 - - + -
90D PHE* 4.0 13.0 - - + -
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Residues in contact with PHE 13 (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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11D GLY* 4.3 0.2 - - - -
12D LEU* 1.3 83.4 - - - +
14D PRO* 1.3 66.0 - - + +
15D ASN 3.3 1.1 - - - +
18D SER* 5.1 0.2 - - - -
20D GLU* 4.5 3.6 - - + -
21D HIS* 3.3 61.7 - + + +
24D PHE* 4.0 20.9 - + - -
41D ILE* 3.9 30.5 - - + -
42D ASP 3.2 10.3 + - - +
43D ILE* 3.3 7.0 - - + -
44D VAL 2.9 26.3 + - - -
46D ILE* 4.3 1.1 - - - -
68D PHE* 3.9 38.1 - + - -
70D PHE* 3.7 21.1 - + - -
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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