Contacts of the strand formed by residues 26 - 34 (chain A) in PDB entry 3SJN
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 ASP 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A HIS* 4.8 1.0 + - - +
12A LEU 3.4 13.2 - - - +
13A ARG* 3.7 23.7 + - + -
21A CYS* 3.7 13.6 - - - -
22A GLU 4.7 0.2 - - - +
24A GLY* 4.3 11.4 + - - -
25A GLU* 1.3 80.2 + - - +
27A ALA* 1.3 63.9 + - - +
45A ASP* 5.5 2.3 - - - +
48A PRO* 3.4 17.7 - - + +
304A SER* 4.7 5.4 + - - -
334A LEU* 3.8 4.7 - - - +
58B PRO* 5.7 0.2 - - - +
60B THR* 2.9 44.7 + - - +
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU 4.4 0.2 - - - -
11A HIS* 3.7 2.3 - - - -
12A LEU* 2.9 39.8 + - + +
26A ASP* 1.3 76.2 - - - +
28A VAL* 1.3 60.9 + - - +
29A ILE* 4.5 9.0 - - + -
43A GLU* 4.5 3.6 - - - +
44A ALA 5.5 1.8 - - - -
48A PRO* 3.8 10.5 - - - +
304A SER* 4.5 6.3 - - - +
305A THR* 4.0 27.1 - - + -
334A LEU* 4.0 10.3 - - + +
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.7 27.6 - - + -
10A LEU 3.4 6.3 - - - +
11A HIS* 5.2 1.1 - - + -
27A ALA* 1.3 74.0 - - - +
29A ILE* 1.3 66.3 + - - +
30A VAL* 5.1 1.6 - - + +
43A GLU* 3.3 20.3 + - - +
44A ALA* 3.3 27.5 + - + +
46A SER 4.7 2.2 - - - +
48A PRO* 3.7 31.0 - - + +
51A VAL* 3.8 38.1 - - + -
52A GLN* 5.2 0.2 - - + -
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLU 3.8 0.3 - - - +
9A VAL* 3.5 3.8 - - - +
10A LEU* 2.8 68.7 + - + +
12A LEU* 4.6 12.6 - - + -
27A ALA* 4.5 11.2 - - + -
28A VAL* 1.3 80.0 - - - +
30A VAL* 1.3 64.0 + - - +
31A LYS* 5.0 3.1 - - + -
41A VAL* 4.8 2.5 - - + -
42A GLY 3.5 8.7 - - - +
43A GLU* 3.9 6.3 - - + +
307A ILE* 3.6 22.4 - - + -
338A LEU* 4.2 12.6 - - + -
362A LEU* 3.8 31.9 - - + -
367A ILE* 4.5 6.1 - - + -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.9 5.2 - - + -
8A GLU 3.3 5.8 - - - +
9A VAL* 4.4 10.1 - - + -
28A VAL* 5.1 4.3 - - + +
29A ILE* 1.3 79.6 - - - +
31A LYS* 1.3 65.7 + - - +
32A VAL* 4.6 3.1 - - + -
40A GLY 3.6 0.2 - - - +
41A VAL* 3.4 7.3 - - - +
42A GLY 2.9 35.2 + - - +
51A VAL* 5.2 0.2 - - + -
55A ILE* 3.8 29.2 - - + -
105A ALA* 3.4 45.8 - - + +
106A ILE* 3.9 12.8 - - + +
109A ALA* 4.2 5.8 - - + -
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.3 3.6 - - - +
8A GLU* 2.7 68.2 + - + +
10A LEU* 4.0 17.6 - - + +
29A ILE* 5.0 1.8 - - + -
30A VAL* 1.3 77.9 - - - +
32A VAL* 1.3 63.3 + - - +
33A HIS* 3.8 15.2 + - - +
39A VAL* 3.8 25.1 - - + -
40A GLY 3.4 3.8 - - - -
41A VAL* 4.6 3.8 - - + -
362A LEU* 4.0 25.5 - - + +
364A GLU* 3.5 30.9 + - - -
367A ILE* 4.8 1.0 - - - +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.8 28.0 - - + -
6A ASP 3.7 2.7 - - - +
7A ILE* 4.0 16.6 - - + -
30A VAL* 4.6 7.6 - - + -
31A LYS* 1.3 73.9 - - - +
33A HIS* 1.3 63.0 + - - +
34A THR* 5.2 0.2 - - + -
39A VAL* 3.3 6.0 - - - -
40A GLY 2.9 30.9 + - - -
106A ILE* 4.4 17.5 - - + +
109A ALA* 3.7 21.8 - - + -
110A LEU* 4.2 12.6 - - + -
113A ILE* 3.5 25.3 - - + +
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Residues in contact with HIS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.4 8.1 - - - +
5A THR* 2.8 33.0 + - - +
6A ASP* 2.9 35.5 + - + +
8A GLU* 2.9 32.5 + - + +
31A LYS* 3.9 22.4 - - + +
32A VAL* 1.3 72.9 - - - +
34A THR* 1.3 62.7 + - - +
38A ILE 4.2 2.2 - - - -
39A VAL* 3.4 30.0 - - + +
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Residues in contact with THR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.7 29.5 - - + +
3A LYS 3.1 14.1 - - - +
4A ILE* 4.5 1.3 - - + -
5A THR* 3.5 9.1 + - - -
33A HIS* 1.3 79.6 - - - +
35A ASP* 1.3 61.0 + - - +
37A GLY* 3.1 19.8 + - - -
38A ILE* 2.5 41.9 + - - +
39A VAL* 5.5 0.2 - - - +
76A ALA* 4.0 11.4 - - + -
113A ILE* 3.8 22.7 - - + -
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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