Contacts of the helix formed by residues 57 - 65 (chain A) in PDB entry 6I3N
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASP 3.9 1.6 + - - -
56A PHE* 1.3 77.4 - - - +
58A TYR* 1.3 69.2 + - - +
59A LEU* 3.3 21.5 - - + +
60A GLU* 3.3 29.1 + - + +
61A ILE* 3.2 20.5 + - - +
23D ALA* 4.1 20.3 - - - +
26D ASN* 6.2 0.2 - - - -
116D TYR* 3.5 30.4 + - + -
119D LYS* 3.4 29.0 + - + +
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Residues in contact with TYR 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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57A GLU* 1.3 77.3 - - - +
59A LEU* 1.3 73.2 + - + +
61A ILE* 3.3 8.5 + - + +
62A ARG* 2.9 48.9 + - + +
65A GLU* 5.7 1.6 - - - -
23D ALA* 4.1 15.8 + - - +
25D LEU 3.7 17.0 - - - +
26D ASN* 4.2 11.4 - - - +
27D MET* 3.6 33.0 - - + -
30D ARG* 3.6 40.1 - - - -
73D ARG* 4.0 4.5 + - - -
76D ASP* 2.4 39.4 + - - -
79D GLN* 4.8 5.8 - - - -
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Residues in contact with LEU 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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57A GLU* 3.3 18.4 - - - +
58A TYR* 1.3 89.7 - - + +
60A GLU* 1.3 62.6 + - - +
62A ARG* 3.7 10.4 - - + +
63A GLN* 2.9 28.1 + - - +
23D ALA* 4.0 24.7 - - + -
79D GLN* 4.8 13.5 - - + +
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Residues in contact with GLU 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 PHE* 4.1 24.5 - - + -
57A GLU* 3.3 43.2 + - + +
59A LEU* 1.3 77.1 - - - +
61A ILE* 1.3 59.1 + - - +
63A GLN* 3.2 10.7 + - - +
64A LEU* 2.9 35.6 + - + +
119D LYS* 4.2 8.4 + - - +
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Residues in contact with ILE 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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47A TRP* 3.5 10.7 - - + -
48A THR* 3.8 30.7 - - + -
51A ALA* 3.7 25.6 - - + -
52A GLU* 4.0 14.4 - - + +
56A PHE* 4.0 17.7 - - + +
57A GLU 3.2 17.4 + - - +
58A TYR* 3.3 8.7 + - - +
60A GLU* 1.3 74.4 - - - +
62A ARG* 1.3 57.8 + - - +
64A LEU* 3.2 8.4 + - + +
65A GLU* 2.9 31.2 + - - +
26D ASN* 5.9 1.1 - - + -
27D MET* 4.0 28.7 - - + +
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Residues in contact with ARG 62 (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 ARG* 5.1 0.8 - - - +
58A TYR* 2.9 43.0 + - + +
59A LEU* 3.7 14.8 - - + +
60A GLU 3.2 0.2 - - - -
61A ILE* 1.3 77.1 - - - +
63A GLN* 1.3 59.1 + - - +
65A GLU* 2.4 45.7 + - - +
66A THR* 3.6 17.4 - - - +
73D ARG* 3.3 42.0 - - - +
76D ASP* 3.8 12.2 + - - +
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Residues in contact with GLN 63 (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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59A LEU 2.9 18.9 + - - +
60A GLU* 3.5 10.9 - - - +
62A ARG* 1.3 75.3 - - - +
64A LEU* 1.3 73.9 + - - +
66A THR* 2.7 33.6 + - + +
67A GLN* 4.2 18.7 + - - +
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Residues in contact with LEU 64 (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 TRP* 3.9 15.5 - - + -
51A ALA* 5.4 0.4 - - + -
56A PHE* 5.2 7.4 - - + -
60A GLU* 2.9 22.8 + - + +
61A ILE* 3.2 9.4 + - + +
63A GLN* 1.3 83.1 - - - +
65A GLU* 1.3 64.1 + - - +
66A THR 3.3 0.5 + - - -
67A GLN* 3.5 35.9 + - - +
70A PRO* 3.3 20.1 - - - +
73A ARG* 3.9 22.7 - - + +
74A LEU* 3.7 36.1 - - + -
77A ALA* 5.0 10.1 - - + -
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Residues in contact with GLU 65 (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 ARG* 2.6 37.6 + - - +
47A TRP* 3.5 24.0 - - + -
48A THR* 4.3 4.5 - - - +
58A TYR* 5.7 1.4 - - - -
61A ILE* 2.9 21.9 + - - +
62A ARG* 2.4 49.7 + - - +
63A GLN 3.2 0.4 - - - -
64A LEU* 1.3 77.2 - - - +
66A THR* 1.3 63.5 + - + +
67A GLN 3.9 4.0 - - - +
70A PRO* 4.6 4.9 - - - +
27D MET* 4.6 6.9 - - - +
73D ARG* 5.5 0.5 + - - -
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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