Contacts of the strand formed by residues 22 - 30 (chain A) 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 SER 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 5.7 2.7 - - - -
15A ILE 3.4 6.3 - - - -
16A ILE* 5.4 6.5 - - - -
20A GLY 4.9 2.0 - - - -
21A GLU* 1.3 80.2 - - - +
23A LEU* 1.3 66.5 + - - +
43A ASN* 3.3 12.8 + - - +
44A ARG* 2.9 30.4 + - - +
45A ILE* 3.0 35.9 - - - +
53B HIS* 5.4 8.1 - - - -
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Residues in contact with LEU 23 (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 VAL* 3.6 7.1 - - - +
15A ILE* 2.9 47.3 + - + +
17A LEU* 4.9 12.8 - - + -
21A GLU* 5.2 9.4 - - - +
22A SER* 1.3 80.1 - - - +
24A ILE* 1.3 67.3 + - - +
25A ALA* 4.3 0.7 - - + -
38A LEU* 4.6 5.6 - - + -
41A VAL* 4.0 18.6 - - + -
42A PHE 3.3 13.9 - - - +
43A ASN* 4.5 2.7 - - - +
44A ARG* 4.5 1.0 - - - +
50A ILE* 3.6 26.7 - - + -
54A GLN* 4.2 11.2 - - - +
56A LEU* 4.0 26.7 - - + -
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Residues in contact with ILE 24 (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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12A ARG* 3.6 27.1 + - + +
13A VAL 3.3 11.4 - - - +
14A VAL* 5.3 4.9 - - + -
23A LEU* 1.3 73.5 - - - +
25A ALA* 1.3 68.2 + - - +
40A ASN 3.6 3.3 - - - +
41A VAL* 3.5 1.7 - - - -
42A PHE* 2.9 36.0 + - + +
43A ASN 5.5 0.2 - - - -
44A ARG* 3.5 56.1 - - + +
47A LYS* 5.7 6.5 - - + -
67A ILE* 5.6 4.9 - - + -
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Residues in contact with ALA 25 (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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12A ARG* 3.2 18.5 - - - +
13A VAL* 2.8 39.1 + - + +
15A ILE* 5.1 3.3 - - + +
23A LEU* 4.3 0.8 - - + -
24A ILE* 1.3 78.0 - - - +
26A SER* 1.3 61.6 + - - +
27A LEU 3.8 0.4 - - - -
38A LEU* 4.2 22.4 - - + -
39A THR 3.5 9.6 - - - +
41A VAL* 3.8 22.4 - - + -
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Residues in contact with SER 26 (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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10A ASN 4.9 8.8 + - - -
11A LYS 3.7 7.5 + - - -
12A ARG* 3.0 24.1 + - - +
25A ALA* 1.3 72.4 - - - +
27A LEU* 1.3 62.3 + - - +
28A ASN* 3.3 4.6 + - - -
38A LEU* 3.5 4.2 - - - -
39A THR* 2.8 56.1 + - - -
40A ASN* 5.0 2.0 - - - +
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Residues in contact with LEU 27 (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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5A LEU* 4.2 16.6 - - + +
8A TYR* 3.6 42.6 - - + +
9A LEU* 3.7 3.4 - - - +
10A ASN* 2.8 29.9 + - - -
11A LYS 3.2 7.9 + - - -
13A VAL* 3.8 18.7 - - + +
25A ALA 3.7 2.8 + - - -
26A SER* 1.3 67.7 - - - +
28A ASN* 1.3 63.1 + - - +
29A GLY 3.4 27.1 - - - +
30A PHE* 4.5 12.1 - - + -
36A LEU* 4.0 20.9 - - + -
37A PHE 4.0 5.8 - - - +
38A LEU* 4.0 11.2 - - + -
64A VAL* 5.4 2.7 - - + -
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Residues in contact with ASN 28 (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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9A LEU* 3.4 24.4 - - - +
10A ASN* 4.1 18.0 + - - +
26A SER* 3.3 7.3 + - - +
27A LEU* 1.3 75.1 - - - +
29A GLY* 1.3 57.6 + - - +
37A PHE* 2.8 40.9 + - + +
39A THR* 2.1 36.3 + - - +
1G MET 4.2 10.0 + - - +
86G ILE* 6.2 0.4 - - - +
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Residues in contact with GLY 29 (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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9A LEU* 5.2 1.1 - - - -
27A LEU* 3.4 9.1 - - - +
28A ASN* 1.3 79.1 - - - +
30A PHE* 1.3 65.7 + - - +
36A LEU* 3.4 0.2 - - - -
37A PHE* 2.6 37.0 + - - +
1G MET 3.5 24.9 - - - -
3G PRO* 4.2 2.0 - - - -
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Residues in contact with PHE 30 (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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4A THR* 4.3 9.0 - - - -
5A LEU* 3.7 44.6 - - + -
6A LYS* 3.6 28.9 - - + -
9A LEU* 3.9 29.6 - - + -
27A LEU* 4.5 7.9 - - + -
29A GLY* 1.3 77.5 - - - +
31A ASP* 1.3 71.3 + - - +
35A ASN 3.1 7.6 - - - -
36A LEU* 3.5 21.5 - - + -
2G LEU* 4.1 12.3 - - - +
3G PRO* 4.0 6.0 - - - +
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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