Contacts of the helix formed by residues 53 - 60 (chain A) in PDB entry 1EZF
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A SER 3.5 0.4 - - - -
52A ARG* 1.3 85.2 - - - +
54A PHE* 1.3 65.0 + - - +
55A ALA* 3.2 4.4 + - - -
56A ALA* 3.5 19.3 + - - +
57A VAL* 4.2 5.9 + - - +
295A MET* 5.1 6.9 - - - +
991A IN0 3.3 18.9 + - - -
340B GLN* 3.3 17.9 + - - +
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Residues in contact with PHE 54 (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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51A SER* 3.3 15.0 + - - +
53A SER* 1.3 79.0 + - - +
55A ALA* 1.3 63.2 + - - +
56A ALA 3.2 0.4 - - - -
57A VAL* 3.1 27.1 + - + +
58A ILE* 3.1 33.2 + - + +
73A TYR* 4.5 2.9 - + - -
288A PHE* 3.3 56.5 - + - -
291A ILE* 4.4 9.9 - - + -
292A PRO* 3.6 26.7 - - + -
295A MET* 6.1 1.6 - - - -
991A IN0 3.5 49.5 + + + +
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Residues in contact with ALA 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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47A LEU* 4.1 19.1 - - + -
48A ASN* 3.2 43.1 - - - +
51A SER* 3.4 17.5 + - - +
52A ARG 6.0 0.2 - - - -
53A SER 3.2 1.7 - - - -
54A PHE* 1.3 77.0 - - - +
56A ALA* 1.3 54.6 + - - +
58A ILE* 3.2 4.0 + - - +
59A GLN* 2.8 40.5 + - - +
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Residues in contact with ALA 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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48A ASN* 4.8 0.6 + - - -
53A SER 3.5 13.3 + - - +
55A ALA* 1.3 79.7 - - - +
57A VAL* 1.3 61.2 + - + +
59A GLN* 4.6 1.5 - - - -
60A ALA* 3.2 19.9 + - - +
336B ALA* 3.4 30.8 - - + +
339B TYR* 3.4 31.7 - - + -
340B GLN* 4.1 13.9 - - + +
343B GLU* 6.2 2.0 - - + +
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Residues in contact with VAL 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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53A SER 4.5 7.4 - - - +
54A PHE* 3.1 32.3 + - + +
56A ALA* 1.3 76.0 - - + +
58A ILE* 1.3 63.5 + - - +
60A ALA* 3.3 16.1 + - + +
61A LEU* 3.7 8.3 + - - +
284A SER 5.2 1.7 - - - +
287A ASN* 4.1 8.5 - - + +
288A PHE* 3.6 35.0 - - + +
291A ILE* 3.7 23.8 - - + -
336B ALA* 4.3 15.5 - - + -
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Residues in contact with ILE 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 TYR* 5.4 0.2 - - + -
47A LEU* 4.0 27.6 - - + -
54A PHE* 3.1 25.1 + - + +
55A ALA* 3.6 6.7 - - - +
57A VAL* 1.3 72.2 - - - +
59A GLN* 1.3 65.7 + - + +
60A ALA 3.0 4.3 - - - -
61A LEU* 2.9 30.2 + - + +
66A ARG* 3.6 8.2 - - + +
69A VAL* 3.9 18.4 - - + -
70A CYS* 4.0 16.6 - - + +
73A TYR* 3.7 34.8 - - + -
288A PHE* 3.4 23.1 - - + -
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Residues in contact with GLN 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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44A TYR* 3.7 30.4 - - + -
47A LEU* 4.4 3.2 - - + +
48A ASN* 2.9 39.2 + - - +
55A ALA* 2.8 22.6 + - - +
56A ALA* 4.7 0.4 - - - -
58A ILE* 1.3 76.0 - - - +
60A ALA* 1.3 56.9 + - - +
61A LEU 3.2 0.2 - - - -
66A ARG* 2.9 43.6 + - - +
339B TYR* 3.5 36.8 - - + +
343B GLU* 5.2 0.9 - - - +
367B ARG* 3.7 26.2 - - - +
370B ASN 3.3 7.4 - - - +
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Residues in contact with ALA 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 ALA 3.2 17.1 + - - +
57A VAL* 3.5 10.3 - - + +
58A ILE 3.0 1.0 - - - -
59A GLN* 1.3 75.8 - - - +
61A LEU* 1.3 62.3 + - - +
62A ASP* 4.4 2.9 - - - +
284A SER* 3.2 16.6 - - - -
332B PRO* 3.4 34.2 - - + +
335B LYS* 3.8 24.5 - - + +
336B ALA* 4.1 4.0 - - + +
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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