Contacts of the strand formed by residues 53 - 62 (chain A) in PDB entry 4II9
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 ILE 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ALA 5.6 0.2 - - - +
13A ARG* 3.7 46.1 - - + +
14A TYR* 3.7 33.9 - - + +
17A PHE* 3.4 40.5 - - + -
45A TYR* 3.9 23.1 - - + -
46A LEU 3.4 7.0 - - - +
47A GLU* 4.3 0.4 - - - +
51A GLY 3.9 0.8 + - - -
52A ALA* 1.4 75.0 - - - +
54A ILE* 1.3 65.6 + - - +
55A ALA 3.5 21.1 - - - +
56A ALA* 4.5 0.7 - - + -
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Residues in contact with ILE 54 (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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17A PHE* 3.6 7.9 - - - -
46A LEU* 2.9 26.2 + - + +
47A GLU 4.0 11.7 - - - +
48A ASP* 3.6 34.1 - - + +
52A ALA* 3.3 2.2 + - + +
53A ILE* 1.3 79.3 - - - +
55A ALA* 1.3 64.0 + - + +
79A MET* 4.4 0.2 - - - +
86A LEU* 3.9 33.7 - - + -
89A ARG* 4.7 5.8 - - - +
402A GOL 2.7 38.8 + - - +
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Residues in contact with ALA 55 (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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17A PHE* 3.7 4.9 - - - -
45A TYR* 3.2 6.9 - - - +
46A LEU* 2.9 34.7 + - + -
53A ILE* 3.5 1.7 - - - +
54A ILE* 1.3 88.3 - - + +
56A ALA* 1.3 62.7 + - - +
78A VAL 3.4 7.6 - - - -
79A MET* 3.7 29.6 - - + -
86A LEU* 4.8 4.7 - - + -
90A LEU* 4.1 11.0 - - + -
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Residues in contact with ALA 56 (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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14A TYR* 3.7 19.7 - - + -
17A PHE* 3.8 17.9 - - + -
18A MET* 3.5 23.9 - - + +
44A VAL 3.4 5.8 - - - +
45A TYR* 4.1 4.0 - - + +
53A ILE* 4.5 0.4 - - + -
55A ALA* 1.3 77.3 - - - +
57A MET* 1.3 60.5 + - - +
77A PRO* 3.5 3.8 - - - +
78A VAL* 2.9 34.9 + - - +
90A LEU* 4.1 4.4 - - - +
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Residues in contact with MET 57 (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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14A TYR* 3.2 3.8 + - - -
28A GLN* 3.7 2.7 - - - +
42A VAL 4.1 0.7 - - - +
43A ASP* 3.4 2.3 - - - -
44A VAL* 2.8 43.5 + - + +
56A ALA* 1.3 75.6 - - - +
58A SER* 1.3 61.0 - - - +
59A MET* 3.7 15.7 + - + +
73A ALA* 3.6 23.6 - - + -
77A PRO* 3.9 28.3 - - + -
90A LEU* 4.0 15.9 - - + +
91A VAL* 4.1 26.2 - - + -
94A ALA* 4.0 7.6 - - + -
105A LEU* 3.8 24.9 - - + -
107A PHE* 4.4 6.7 - - + -
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Residues in contact with SER 58 (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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14A TYR* 2.7 24.8 + - - -
18A MET* 3.5 1.6 - - - +
27A THR 5.1 1.3 - - - +
28A GLN* 2.7 62.4 + - - -
29A ASP 5.0 2.5 - - - -
30A LEU* 4.0 3.9 - - - +
43A ASP* 3.1 15.3 + - - -
57A MET* 1.3 70.7 - - - +
59A MET* 1.4 61.1 + - - +
60A LEU* 5.7 0.9 - - - -
72A TYR 4.0 0.3 - - - +
73A ALA* 3.3 10.2 - - - -
74A SER 4.5 0.2 + - - -
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Residues in contact with MET 59 (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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41A PRO* 3.4 5.2 - - - +
42A VAL* 2.8 69.7 + - + +
43A ASP* 3.9 2.4 - - - +
44A VAL* 4.3 9.6 - - + -
57A MET* 3.9 12.8 - - + +
58A SER* 1.4 77.8 - - - +
60A LEU* 1.3 65.8 + - - +
61A LEU* 4.1 11.7 - - + -
72A TYR 3.4 9.2 - - - +
73A ALA* 4.3 0.9 - - + -
94A ALA* 3.8 39.5 - - + +
98A LEU* 4.0 16.2 - - + -
105A LEU* 3.5 31.0 - - + -
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Residues in contact with LEU 60 (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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27A THR 5.6 1.3 - - - +
32A TRP* 4.1 19.5 - - + +
33A ALA* 3.8 24.5 - - + +
36A LYS* 3.7 32.3 - - + +
39A TRP* 3.5 36.4 - - + +
40A GLU 3.3 1.1 - - - +
41A PRO* 3.8 18.4 - - + -
58A SER 5.7 0.9 - - - -
59A MET* 1.3 80.5 - - - +
61A LEU* 1.4 63.6 + - - +
70A PHE 3.5 2.4 - - - +
72A TYR* 2.9 37.2 + - + +
74A SER* 6.2 2.7 - - - -
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Residues in contact with LEU 61 (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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38A ASN 4.7 0.3 - - - +
39A TRP* 3.4 8.5 - - - -
40A GLU* 2.8 48.5 + - + +
42A VAL* 3.9 15.7 - - + -
59A MET* 4.1 7.2 - - + -
60A LEU* 1.4 82.6 - - - +
62A GLY* 1.3 61.6 - - - +
69A LYS* 4.3 23.9 - - + +
70A PHE 3.2 3.4 - - - +
71A ALA* 3.9 17.7 - - + -
98A LEU* 3.8 29.4 - - + -
101A ARG* 3.8 37.7 - - + +
102A ALA* 5.1 1.1 - - + -
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Residues in contact with GLY 62 (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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38A ASN 5.5 2.2 - - - -
39A TRP* 3.4 27.2 - - - -
61A LEU* 1.3 75.3 - - - +
63A ASP* 1.3 68.3 + - - -
69A LYS* 3.3 9.5 - - - -
70A PHE* 2.8 37.4 + - - -
101B UDP 6.1 0.2 - - - -
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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