Contacts of the helix formed by residues 38 - 45 (chain A) in PDB entry 7ACN
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 LEU 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A THR* 1.3 70.8 - - - +
39A SER* 1.3 62.9 + - - +
41A LYS* 3.1 13.3 + - + +
42A ILE* 3.1 35.5 + - + +
175A GLY 5.3 1.3 - - - +
239A GLU* 2.9 20.8 + - + +
269A VAL* 4.1 14.6 - - + -
270A PHE 3.6 12.1 - - - +
271A PRO* 3.5 37.5 - - + -
272A TYR 4.9 0.2 - - - +
298A HIS 4.1 3.8 - - - +
299A LEU* 3.4 32.1 - - - +
300A VAL 3.8 3.4 - - - +
301A PRO* 3.6 18.0 - - + +
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Residues in contact with SER 39 (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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37A THR* 3.2 9.9 + - - -
38A LEU* 1.3 72.1 - - - +
40A GLU* 1.3 59.5 + - - +
42A ILE* 3.4 0.3 + - - -
43A VAL* 2.9 36.7 + - - +
177A ILE* 4.0 17.9 - - - -
200A PRO* 5.9 0.3 - - - +
202A VAL* 3.6 18.4 - - - +
237A ILE* 3.6 34.3 - - - +
239A GLU* 2.9 19.9 + - - -
269A VAL* 4.3 2.9 - - - +
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Residues in contact with GLU 40 (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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34A ARG* 2.8 45.5 + - - -
36A LEU* 3.5 6.5 - - + -
37A THR* 3.0 34.5 + - - +
39A SER* 1.3 76.5 + - - +
41A LYS* 1.3 61.3 + - - +
43A VAL* 4.7 0.7 - - - -
44A TYR* 2.8 71.0 + - + +
57A ARG* 3.0 27.1 + - - +
200A PRO 6.1 0.2 - - - +
202A VAL* 4.5 4.7 - - + -
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Residues in contact with LYS 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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21A LEU* 4.0 0.2 - - - +
25A ILE* 3.5 27.4 - - + +
29A ARG* 3.7 10.0 - - - +
36A LEU* 4.0 18.8 - - + +
37A THR 3.0 16.1 + - - +
38A LEU* 3.1 8.5 + - - +
40A GLU* 1.3 75.1 - - - +
42A ILE* 1.3 58.7 + - + +
44A TYR* 5.2 0.2 - - - -
45A GLY* 2.8 28.8 + - - -
297A ASP 2.7 20.0 + - - -
298A HIS* 3.6 21.8 - - - +
300A VAL* 2.7 30.3 + - - +
301A PRO 3.8 1.8 + - - -
302A ASP* 2.8 43.0 + - - +
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Residues in contact with ILE 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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21A LEU* 4.2 7.9 - - + -
38A LEU* 3.1 39.4 + - + +
41A LYS* 1.3 73.9 - - - +
43A VAL* 1.3 65.9 + - - +
45A GLY 3.4 1.0 + - - -
46A HIS* 2.7 34.2 + - - +
158A GLY* 3.6 33.2 - - - +
159A VAL 3.7 11.4 - - - +
160A LEU* 5.1 0.9 - - + -
175A GLY 3.4 27.4 - - - +
176A GLY* 4.6 0.2 - - - -
177A ILE* 3.7 31.4 - - + -
269A VAL* 4.7 1.3 - - + -
298A HIS 4.8 6.5 - - - +
299A LEU* 5.2 2.0 - - + -
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Residues in contact with VAL 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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39A SER 2.9 22.5 + - - +
40A GLU* 4.4 1.1 - - - +
42A ILE* 1.3 76.9 - - - +
44A TYR* 1.4 68.5 + - + +
46A HIS* 2.9 13.8 + - - -
62A LEU* 3.7 29.6 - - + -
64A LEU* 3.3 33.5 - - + +
160A LEU* 5.2 5.4 - - + -
177A ILE* 3.8 29.6 - - + -
179A ILE* 5.5 2.9 - - + -
197A LEU* 5.1 2.2 - - + -
200A PRO* 5.1 7.4 - - + -
237A ILE* 4.2 15.7 - - + -
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Residues in contact with TYR 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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24A ASN* 4.1 7.1 - - - +
25A ILE* 6.0 1.8 - - + -
28A VAL* 3.7 36.0 - - + +
32A LEU* 4.2 3.6 - - + -
34A ARG* 4.3 0.2 + - - -
36A LEU* 4.2 10.3 - - + -
40A GLU* 2.8 69.0 + - + +
41A LYS* 4.7 0.7 - - - +
43A VAL* 1.4 82.7 - - + +
45A GLY* 1.3 60.9 + - - +
46A HIS 3.1 1.2 + - - -
47A LEU* 3.2 31.3 + - + +
50A PRO* 4.8 0.2 - - - +
55A ILE* 3.4 36.5 - - + +
57A ARG* 4.3 5.7 - - - +
62A LEU* 4.0 22.9 - - + -
199A CYS* 3.5 14.3 - - - -
200A PRO* 5.2 2.3 + - + -
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Residues in contact with GLY 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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20A LEU 4.8 0.2 - - - -
21A LEU* 3.8 22.4 + - - +
24A ASN* 3.0 33.7 + - - +
25A ILE* 4.1 9.1 - - - +
41A LYS 2.8 22.5 + - - -
42A ILE 3.8 2.2 - - - -
43A VAL 3.1 0.2 - - - -
44A TYR* 1.3 77.0 - - - +
46A HIS* 1.3 58.6 + - - +
47A LEU 3.5 0.7 - - - -
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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