Contacts of the strand formed by residues 40 - 48 (chain A) in PDB entry 6V65
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 SER 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ARG* 3.3 4.7 - - - +
19A ALA 2.7 43.8 + - - -
20A VAL* 4.7 0.2 - - - +
21A VAL* 4.5 9.4 - - - +
38A GLY 4.2 3.5 + - - -
39A LEU* 1.3 77.5 + - - +
41A SER* 1.3 60.2 + - - +
42A VAL* 3.9 5.4 - - - -
62A GLY* 4.4 3.8 - - - -
63A GLU 3.2 19.1 - - - -
64A ARG* 3.6 11.1 + - - +
65A LEU* 4.2 4.7 - - - -
71A VAL* 3.5 24.3 - - - +
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Residues in contact with SER 41 (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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16A ARG* 5.5 11.6 + - - -
17A VAL 3.3 10.3 - - - -
18A ARG* 4.2 10.5 - - - +
40A SER* 1.3 72.3 - - - +
42A VAL* 1.3 62.7 + - - +
43A THR* 3.8 9.4 + - - +
61A ARG 3.7 1.4 - - - +
62A GLY* 3.5 14.9 - - - -
63A GLU* 3.1 25.5 + - - +
65A LEU* 3.7 19.3 - - - +
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Residues in contact with VAL 42 (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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16A ARG* 3.6 3.6 - - - -
17A VAL* 2.9 33.1 + - + +
19A ALA* 4.5 13.5 - - + +
21A VAL* 5.6 2.7 - - + -
40A SER* 4.4 13.0 - - - +
41A SER* 1.3 73.9 - - - +
43A THR* 1.3 63.3 + - - +
60A ILE* 3.7 18.8 - - + -
61A ARG 3.3 8.1 - - - +
62A GLY* 4.2 7.0 - - - -
72A LEU* 5.9 2.5 - - + -
101A LEU* 3.8 30.5 - - + -
112A PHE* 3.6 34.2 - - + -
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Residues in contact with THR 43 (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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13A SER* 4.7 7.9 - - - -
15A ALA 3.6 5.4 - - - +
16A ARG* 3.8 38.6 - - + +
41A SER* 4.4 9.0 - - - +
42A VAL* 1.3 79.0 - - - +
44A VAL* 1.3 65.0 + - - +
45A PHE* 3.7 22.7 - - - -
59A PHE 4.0 0.2 - - - +
60A ILE* 3.5 6.4 - - - +
61A ARG* 2.7 47.3 + - - +
63A GLU* 6.1 0.4 - - - +
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Residues in contact with VAL 44 (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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13A SER* 3.2 5.1 - - - -
14A TYR* 2.5 52.8 + - + -
15A ALA* 3.3 12.6 + - + +
43A THR* 1.3 77.5 - - - +
45A PHE* 1.3 60.7 + - - +
58A PHE* 5.9 0.2 - - + -
59A PHE 3.5 10.5 - - - +
60A ILE* 4.6 5.4 - - + -
76A LEU* 4.1 7.0 - - + -
112A PHE* 3.6 23.3 - - + -
116A ILE* 3.5 31.9 - - + -
119A ALA* 4.1 20.6 - - + -
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Residues in contact with PHE 45 (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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13A SER* 4.3 14.1 - - - +
14A TYR* 4.4 9.0 - - - -
43A THR* 3.7 17.0 - - - -
44A VAL* 1.3 78.6 - - - +
46A LYS* 1.3 70.3 + - - +
47A VAL* 4.0 13.2 - - + -
57A ASP 4.1 0.2 - - - +
58A PHE* 3.5 7.0 - - - +
59A PHE* 3.1 56.4 + + + -
61A ARG* 3.5 49.8 - - + -
73A GLU* 5.2 2.2 - - - -
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Residues in contact with LYS 46 (chain A).
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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14A TYR* 3.7 29.4 + - + +
45A PHE* 1.3 81.3 - - - +
47A VAL* 1.3 66.4 + - - +
48A PRO* 4.0 9.0 - - + +
52A GLU 4.0 20.9 + - - -
53A ASN* 5.4 2.8 - - - +
54A GLY 4.9 5.5 + - - -
56A ALA* 4.2 15.9 - - + -
57A ASP 3.2 6.5 - - - +
58A PHE* 3.5 26.5 - - + -
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Residues in contact with VAL 47 (chain A).
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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45A PHE* 4.0 16.8 - - + -
46A LYS* 1.3 77.5 - - - +
48A PRO* 1.3 78.5 - - + +
49A HIS* 3.5 2.3 + - - -
56A ALA* 3.3 2.2 - - - -
57A ASP* 2.8 31.2 + - + +
59A PHE* 3.6 28.5 - - + -
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Residues in contact with PRO 48 (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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46A LYS* 4.0 10.8 - - + +
47A VAL* 1.3 96.6 - - + +
49A HIS* 1.3 65.9 + - - +
50A GLN 4.2 4.5 - - - +
51A GLU 3.5 24.5 - - - +
52A GLU* 3.3 39.9 - - - +
54A GLY 5.2 0.2 - - - +
55A CYS 3.7 1.6 - - - +
56A ALA* 3.6 11.8 - - + -
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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