Contacts of the strand formed by residues 24 - 32 (chain I) in PDB entry 4M7A
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 GLU 24 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I VAL* 3.9 13.3 - - + +
17I VAL 3.6 10.1 - - - +
18I GLU* 4.3 16.5 - - + +
22I ASP 4.4 1.1 - - - +
23I ILE* 1.3 77.0 - - - +
25I ILE* 1.3 67.3 + - - +
46I THR* 2.8 31.9 + - - +
50I LYS* 2.5 53.8 + - + +
51I TYR* 3.2 25.6 - - - +
71I TYR* 4.8 2.5 - - - -
61J ARG* 3.5 28.1 + - - -
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Residues in contact with ILE 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H LEU* 3.7 29.8 - - + -
15I VAL 3.9 0.3 - - - +
16I VAL* 3.7 3.9 - - - -
17I VAL* 2.9 42.3 + - + +
19I LEU* 5.1 2.5 - - + -
23I ILE* 4.3 10.8 - - + -
24I GLU* 1.3 85.3 - - - +
26I LYS* 1.3 72.8 + - - +
40I LEU* 4.0 9.8 - - + +
43I ILE* 4.2 8.5 - - + -
44I SER 4.0 6.7 - - - +
46I THR* 5.2 0.4 - - - -
51I TYR* 4.2 5.6 - - + -
52I PRO* 4.2 17.5 - - + -
60I ILE* 3.7 26.2 - - + -
62I ILE* 4.6 9.2 - - + -
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Residues in contact with LYS 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I GLU* 2.7 37.9 - - - +
15I VAL 3.4 8.7 - - - +
16I VAL* 4.4 11.4 - - + +
25I ILE* 1.3 83.5 - - - +
27I GLY* 1.3 57.0 + - - +
40I LEU* 4.3 1.5 - - - +
42I ASN 4.4 0.4 - - - -
43I ILE* 3.8 2.8 - - - -
44I SER* 2.9 56.4 + - - +
45I SER 4.2 7.1 + - - -
46I THR* 3.5 28.6 - - + +
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Residues in contact with GLY 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I GLN 3.5 0.5 - - - +
14I GLU* 3.1 10.9 - - - -
15I VAL* 2.9 36.0 + - - +
26I LYS* 1.3 79.2 - - - +
28I THR* 1.3 62.9 + - - -
29I LEU 3.7 0.9 + - - -
40I LEU* 4.2 14.9 - - - +
41I ASP 3.8 2.2 - - - -
42I ASN 3.8 13.0 - - - -
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Residues in contact with THR 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I ASP* 3.6 26.5 - - - +
13I GLN 3.0 16.8 - - - +
14I GLU* 3.8 12.5 + - + +
27I GLY* 1.3 70.7 - - - -
29I LEU* 1.3 61.3 + - - +
30I GLN* 2.9 12.1 + - - +
40I LEU* 3.2 2.8 - - - -
41I ASP* 2.8 46.6 + - - +
42I ASN* 4.0 10.9 + - - +
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Residues in contact with LEU 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I PHE* 3.4 33.7 - - + +
10I LEU* 3.3 33.7 - - + +
11I VAL* 3.3 9.3 - - + +
12I ASP* 2.9 26.7 + - - -
13I GLN* 2.7 12.6 + - + +
15I VAL* 4.7 15.0 - - + +
27I GLY 3.7 2.8 + - - -
28I THR* 1.3 66.7 - - - +
30I GLN* 1.3 58.5 + - - +
31I SER 3.9 17.0 - - - +
32I VAL* 3.9 15.5 - - + -
38I LEU* 4.2 15.9 - - + -
39I LYS 3.4 14.8 - - - +
40I LEU* 3.8 11.8 - - + +
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Residues in contact with GLN 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H ASP* 4.9 10.7 + - - -
11I VAL* 3.7 16.4 - - - +
28I THR* 2.9 8.6 + - + +
29I LEU* 1.3 74.5 - - - +
31I SER* 1.3 77.8 + - - +
39I LYS* 2.9 21.7 + - - +
41I ASP* 3.5 23.5 - - - +
59I ASN* 2.3 35.9 + - - -
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Residues in contact with SER 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H THR 5.5 5.1 + - - -
11I VAL* 5.4 3.1 - - - -
29I LEU* 3.6 5.7 - - - +
30I GLN* 1.3 94.0 + - - +
32I VAL* 1.3 70.0 + - - +
37I ASN 3.9 0.2 - - - +
38I LEU* 3.9 2.6 - - - -
39I LYS* 3.1 47.4 + - - +
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Residues in contact with VAL 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I PHE* 3.1 29.9 - - + +
7I PHE* 3.4 55.9 - - + +
8I LYS* 4.4 9.5 - - + +
11I VAL* 5.6 3.1 - - + +
29I LEU* 3.9 13.5 - - + -
31I SER* 1.3 82.9 + - - +
33I ASP* 1.3 77.9 + - - +
36I LEU* 5.2 2.0 - - + -
37I ASN 3.8 2.5 - - - +
38I LEU* 4.0 9.4 - - + -
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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