Contacts of the helix formed by residues 54 - 61 (chain A) in PDB entry 4L1O
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 ASN 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.1 6.3 - - - -
48A ALA* 5.4 0.2 - - - -
53A LYS* 1.3 74.4 - - - +
55A GLU* 1.3 66.0 + - - +
56A TRP* 2.9 19.5 + - - +
57A ASN* 2.8 27.3 + - - +
58A ALA* 2.9 26.5 + - - +
279A ARG* 2.8 38.7 + - + +
280A ASP* 2.9 24.3 + - - +
445B SER* 3.9 3.4 + - - -
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Residues in contact with GLU 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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40A GLU* 5.0 8.9 - - - +
41A GLN* 3.3 29.5 + - - +
44A VAL* 3.7 35.1 - - + +
54A ASN* 1.3 76.0 - - - +
56A TRP* 1.3 62.6 - - - +
58A ALA* 3.8 2.8 - - - +
59A TYR* 3.7 16.5 + - - +
449B MET* 3.3 39.2 - - + +
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Residues in contact with TRP 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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54A ASN* 2.9 10.5 + - - +
55A GLU* 1.3 78.4 - - - +
57A ASN* 1.3 81.1 + - + +
59A TYR* 3.2 3.5 + - - -
60A TYR* 2.9 80.1 + + + -
61A GLU* 3.9 23.3 - - + -
280A ASP* 5.2 0.7 - - - -
440B VAL* 3.6 27.4 - - + +
441B ARG* 3.7 26.5 - - + -
442B TYR 5.6 2.0 - - - -
443B PRO* 6.5 0.4 - - + -
445B SER* 3.6 26.2 - - - +
446B PRO* 3.5 30.0 - - + +
449B MET* 4.0 23.1 - - + -
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Residues in contact with ASN 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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52A HIS 5.3 0.8 + - - -
53A LYS* 3.3 25.4 + - - +
54A ASN* 2.8 52.4 + - - +
56A TRP* 1.3 85.8 - - + +
58A ALA* 1.3 73.5 + - - +
61A GLU* 3.0 56.0 + - - +
62A GLU* 4.5 1.0 - - - +
279A ARG 4.7 0.2 + - - -
280A ASP* 3.9 23.2 + - - +
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Residues in contact with ALA 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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44A VAL* 3.8 29.4 - - + +
47A LEU* 3.9 26.9 - - + +
53A LYS* 4.8 4.7 - - + +
54A ASN 2.9 20.4 + - - +
55A GLU 3.8 1.6 - - - +
57A ASN* 1.3 81.7 + - - +
59A TYR* 1.3 55.1 + - - +
62A GLU* 3.4 7.1 - - - +
63A VAL* 3.1 30.6 + - + +
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Residues in contact with TYR 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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36A ILE* 5.2 1.6 - - + -
40A GLU* 4.2 8.5 - - + +
44A VAL* 6.2 1.1 - - + -
55A GLU 3.7 9.3 + - - +
56A TRP 3.2 6.9 + - - +
57A ASN 3.2 0.4 - - - -
58A ALA* 1.3 79.2 - - - +
60A TYR* 1.3 90.8 + + + +
61A GLU 3.3 0.2 - - - -
63A VAL* 3.2 26.5 + - + -
64A VAL* 2.8 52.9 + - + +
67A LEU* 3.5 33.9 - - + +
452B HIS* 3.6 56.1 - + + +
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Residues in contact with TYR 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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56A TRP* 2.9 81.7 + + + +
59A TYR* 1.3 99.9 - + + +
61A GLU* 1.3 62.0 + - - +
62A GLU 3.6 0.2 - - - -
64A VAL* 4.0 14.1 - - + +
65A TYR* 3.5 18.2 + - - -
449B MET* 6.2 1.3 - - - -
450B THR* 4.8 7.4 + - - -
451B GLN 4.8 4.9 + - - -
452B HIS* 3.9 21.2 + + - -
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Residues in contact with GLU 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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53A LYS* 4.5 10.1 + - - +
56A TRP* 3.9 17.1 - - + -
57A ASN* 3.0 39.1 + - + +
60A TYR* 1.3 81.5 - - - +
62A GLU* 1.3 62.0 + - - +
65A TYR* 3.7 12.4 - - - +
115A TYR* 3.5 22.6 + - + -
233A TRP* 4.4 8.5 + - + +
237A MET* 4.1 38.3 - - + +
238A ASN 4.7 2.4 + - - -
601A 1VL 3.6 18.3 + - - -
441B ARG 4.6 2.4 - - - +
443B PRO* 5.8 3.8 - - - +
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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