Contacts of the strand formed by residues 65 - 76 (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 MET 65 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C LEU* 4.3 2.0 - - - -
32D LEU* 4.5 22.4 - - + -
42D VAL* 4.8 2.9 - - + -
44D ILE* 3.6 25.4 - - + -
56D VAL* 3.5 24.0 - - + -
58D ALA 3.3 5.8 - - - +
59D PHE* 3.9 15.3 - - + -
63D CYS* 3.2 13.8 + - - +
64D ASN* 1.3 79.9 - - - +
66D VAL* 1.3 61.7 + - - +
67D LEU* 3.5 32.8 - - + -
100D PHE* 3.4 6.6 - - - -
101D LEU* 2.8 37.0 + - + +
106D VAL* 4.9 5.8 - - - -
109D VAL* 4.8 8.5 - - + -
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Residues in contact with VAL 66 (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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3C LEU* 4.4 9.4 - - + +
6C PHE* 4.2 19.5 - - + -
70C LEU* 5.2 1.3 - - + -
76C LEU* 4.2 26.0 - - + -
80C LEU* 4.7 11.4 - - + -
56D VAL* 3.7 0.7 - - - -
57D LYS* 2.9 42.0 + - + -
58D ALA* 3.0 18.6 + - + +
65D MET* 1.3 73.4 - - - +
67D LEU* 1.3 67.7 - - - +
98D LYS* 6.1 0.2 - - + -
99D MET 3.3 10.5 - - - +
100D PHE* 3.8 25.1 - - + -
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Residues in contact with LEU 67 (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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42D VAL* 6.1 0.4 - - + -
44D ILE* 3.9 22.0 - - + -
52D LEU* 4.5 10.5 - - + -
54D GLY* 5.2 4.0 - - - +
55D ARG 3.1 21.3 - - - +
56D VAL* 4.0 1.6 - - + -
57D LYS* 5.1 0.4 - - - -
65D MET* 3.5 35.0 - - + +
66D VAL* 1.3 82.7 - - - +
68D GLU* 1.3 64.7 + - - +
70D VAL* 3.4 23.3 - - + -
98D LYS* 3.4 4.5 - - - +
99D MET* 2.9 55.0 + - + +
101D LEU* 4.5 9.0 - - + -
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Residues in contact with GLU 68 (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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76C LEU* 3.8 20.4 - - + +
54D GLY* 3.8 0.9 - - - -
55D ARG* 2.9 36.2 + - + +
57D LYS* 3.3 43.1 + - + +
67D LEU* 1.3 74.3 - - - +
69D ASN* 1.3 90.7 + - - +
70D VAL* 3.2 3.6 + - - +
97D SER 3.2 9.5 - - - +
98D LYS* 4.0 14.7 - - + -
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Residues in contact with ASN 69 (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* 5.2 4.5 + - - -
53D LEU 3.6 8.1 - - - +
54D GLY* 3.7 4.3 - - - -
55D ARG* 4.3 21.8 - - + +
68D GLU* 1.3 94.9 + - - +
70D VAL* 1.3 63.9 + - - +
71D LYS* 3.9 0.7 + - - +
95D TYR* 5.9 2.0 - - - -
96D ILE 3.8 4.3 - - - -
97D SER* 2.9 23.9 + - - +
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Residues in contact with VAL 70 (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 LEU* 3.7 28.7 - - + -
53D LEU 3.3 9.4 - - - +
54D GLY* 4.5 3.1 - - - -
67D LEU* 3.4 35.2 - - + +
68D GLU 3.8 10.3 - - - +
69D ASN* 1.3 76.7 - - - +
71D LYS* 1.3 68.2 + - - +
72D GLU 4.0 2.5 - - - +
95D TYR* 3.5 7.9 - - - +
96D ILE* 2.8 36.0 + - + +
99D MET* 3.5 32.5 - - + +
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Residues in contact with LYS 71 (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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51D LYS 3.2 4.5 - - - +
53D LEU* 2.9 41.7 + - + +
69D ASN 5.2 0.7 - - - +
70D VAL* 1.3 75.3 - - - +
72D GLU* 1.3 60.9 + - - +
73D MET* 3.5 38.2 - - + +
93D ASP* 3.9 20.0 + - + -
94D ARG 3.4 5.8 - - - +
95D TYR* 2.8 44.6 + - + +
47K GLU* 3.3 23.8 + - + +
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Residues in contact with GLU 72 (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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67C TYR* 2.4 31.6 + - - -
48D ASN* 4.1 1.2 + - - -
50D LYS* 3.2 33.5 + - + +
51D LYS 3.2 4.7 - - - -
52D LEU* 3.9 18.1 - - + +
70D VAL* 4.0 2.2 - - + +
71D LYS* 1.3 72.5 - - - +
73D MET* 1.3 61.5 + - - +
74D TRP* 3.8 11.9 - - + -
93D ASP* 3.1 6.4 - - - +
94D ARG* 2.5 80.3 + - + +
96D ILE* 4.6 7.6 - - + +
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Residues in contact with MET 73 (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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43D LEU* 5.3 0.9 - - - -
50D LYS* 3.5 0.6 - - - -
51D LYS* 2.6 51.8 + - + +
53D LEU* 4.8 8.3 - - - -
71D LYS* 3.5 36.6 - - + +
72D GLU* 1.3 80.7 - - - +
74D TRP* 1.3 63.0 + - - +
92D LYS 3.4 7.6 - - - +
93D ASP* 4.2 5.8 - - + +
44K TYR* 3.9 33.9 - - + -
47K GLU* 3.4 46.2 - - + +
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Residues in contact with TRP 74 (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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49D ASN 4.4 5.4 - - - +
50D LYS* 3.1 49.4 - - + +
51D LYS* 5.7 0.2 - - - -
72D GLU* 3.8 37.9 - - + -
73D MET* 1.3 73.7 - - - +
75D THR* 1.3 65.4 + - - +
76D GLU* 3.0 36.8 + - + +
91D ASN* 3.7 3.7 - - - +
92D LYS* 2.8 62.9 + - + +
93D ASP* 3.9 5.4 - - - -
94D ARG* 3.8 26.2 - - + -
44K TYR* 4.5 9.7 + - - -
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Residues in contact with THR 75 (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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49D ASN* 5.5 5.8 + - - +
74D TRP* 1.3 79.9 - - - +
76D GLU* 1.3 67.3 + - - +
89D PRO* 3.9 20.4 - - + +
90D VAL 3.3 13.4 + - - -
91D ASN* 4.4 7.4 + - - -
36K GLN* 2.9 28.9 + - + +
39K CYS* 5.5 11.7 - - - -
44K TYR* 4.9 8.5 + - - +
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Residues in contact with GLU 76 (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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1381 G 5.5 3.1 - - - +
74D TRP* 3.0 32.0 + - + +
75D THR* 1.3 79.5 - - - +
77D VAL* 1.3 62.7 + - + +
89D PRO* 3.2 7.2 - - - +
90D VAL* 2.6 49.4 + - + +
92D LYS* 3.5 29.0 + - + -
36K GLN* 4.3 8.3 - - - +
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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