Contacts of the strand formed by residues 51 - 59 (chain D) in PDB entry 4PJO
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 LYS 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D LEU* 4.5 8.5 - - + -
44D ILE 3.6 2.0 - - - +
45D ASN* 3.0 16.3 + - - +
49D ASN* 4.1 9.2 + - - +
50D LYS* 1.3 72.4 - - - +
52D LEU* 1.3 61.4 + - - +
71D LYS 3.2 4.7 - - - +
72D GLU* 3.2 1.3 - - - -
73D MET* 2.6 53.1 + - + +
74D TRP* 5.7 0.2 - - - -
39K CYS* 2.8 34.1 + - - -
40K GLY 3.1 18.3 + - - -
41K ILE* 3.0 41.1 - - + +
44K TYR* 3.5 34.7 + - + +
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Residues in contact with LEU 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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67C TYR* 4.5 12.3 - - + -
42D VAL 3.6 1.7 - - - +
43D LEU* 3.4 2.3 - - - +
44D ILE* 2.8 51.7 + - + +
46D CYS* 4.1 20.9 - - + -
50D LYS* 5.0 4.0 - - + +
51D LYS* 1.3 72.2 - - - +
53D LEU* 1.3 61.0 + - - +
54D GLY 4.1 0.2 + - - -
67D LEU* 4.5 9.9 - - + -
70D VAL* 3.7 17.3 - - + -
71D LYS 3.5 3.1 - - - -
72D GLU* 3.9 35.4 - - + +
99D MET* 4.5 9.6 - - + -
101D LEU* 3.6 32.3 - - + -
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Residues in contact with LEU 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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41D GLN* 3.3 32.6 + - + +
42D VAL 3.0 22.9 - - - +
43D LEU* 3.9 17.5 - - + +
51D LYS 4.0 0.2 + - - -
52D LEU* 1.3 73.4 - - - +
54D GLY* 1.3 61.3 + - - +
69D ASN 3.6 2.4 - - - +
70D VAL* 3.3 2.3 - - - -
71D LYS* 2.9 45.5 + - + +
73D MET* 4.8 4.9 - - - -
44K TYR 5.0 0.7 - - - +
47K GLU* 3.4 46.4 - - + +
48K PHE* 3.7 15.3 - - + +
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Residues in contact with GLY 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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41D GLN* 3.3 8.0 - - - -
42D VAL* 2.6 41.9 + - - +
44D ILE* 6.3 0.2 - - - +
52D LEU 4.1 0.8 - - - -
53D LEU* 1.3 78.1 - - - +
55D ARG* 1.3 63.7 - - - -
67D LEU* 5.2 5.3 - - - +
68D GLU 3.8 2.5 - - - -
69D ASN 3.7 13.2 - - - -
70D VAL* 4.1 7.8 - - - +
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Residues in contact with ARG 55 (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 ASN* 2.7 40.8 + - - +
40D THR 4.2 6.3 - - - +
41D GLN* 3.4 20.3 - - + +
54D GLY* 1.3 76.9 - - - +
56D VAL* 1.3 64.5 + - - +
57D LYS* 3.8 2.9 + - + -
67D LEU* 3.1 9.4 - - - +
68D GLU* 2.9 45.7 + - + +
69D ASN* 4.3 19.5 - - + +
49K GLU* 2.6 44.4 + - - -
55K PRO* 3.3 26.1 - - - +
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Residues in contact with VAL 56 (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 LEU* 5.3 4.9 - - + -
35D SER* 4.3 10.0 + - - +
36D VAL* 3.5 39.0 - - + +
39D ASN* 5.4 3.2 - - - +
40D THR 4.5 3.6 + - - +
42D VAL* 3.6 29.8 - - + -
55D ARG* 1.3 76.0 - - - +
57D LYS* 1.3 62.4 + - - +
58D ALA 3.6 21.1 - - - +
59D PHE* 4.6 3.8 - - + -
65D MET* 3.5 38.8 - - + -
66D VAL 3.7 3.4 - - - +
67D LEU* 4.0 1.3 - - + -
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Residues in contact with LYS 57 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-2C SER 5.2 0.5 - - - +
76C LEU* 4.2 15.7 - - + +
77C ASP* 2.7 37.8 + - - -
80C LEU* 4.4 11.4 - - + +
36D VAL* 3.9 13.9 - - - +
39D ASN* 6.4 0.9 - - - +
55D ARG* 3.8 3.1 + - + +
56D VAL* 1.3 75.9 - - - +
58D ALA* 1.3 64.5 + - - +
66D VAL* 2.9 24.9 + - + +
68D GLU* 3.3 45.0 + - + +
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Residues in contact with ALA 58 (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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-2C SER 4.6 9.2 - - - +
0C SER* 4.7 5.2 - - - +
3C LEU* 4.2 12.3 - - + -
80C LEU* 4.2 27.8 - - + -
36D VAL* 4.3 6.1 - - - -
56D VAL* 3.4 6.7 - - - +
57D LYS* 1.3 82.3 - - - +
59D PHE* 1.3 67.3 + - - +
65D MET* 3.3 2.8 - - - -
66D VAL* 3.0 28.3 + - + +
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Residues in contact with PHE 59 (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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-2C SER 4.0 1.6 - - - -
-1C GLY* 2.9 49.8 - - - -
0C SER* 3.0 9.4 + - - -
3C LEU* 3.9 5.8 - - - -
24D PHE* 4.1 23.1 - + - -
29D LEU* 3.8 17.0 - - + -
32D LEU* 3.3 42.0 - - + -
33D THR* 3.4 28.0 - - + -
36D VAL* 3.9 14.1 - - + -
56D VAL* 4.6 0.9 - - + -
58D ALA* 1.3 78.2 - - - +
60D ASP* 1.3 74.0 + - - +
64D ASN 3.1 15.3 - - - +
65D MET* 3.9 12.1 - - + -
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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