Contacts of the helix formed by residues 58 - 66 (chain A) in PDB entry 3L6D
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 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A TRP* 3.5 14.1 - - - +
56A CYS* 3.3 4.9 + - - +
57A GLU* 1.3 87.5 + - - +
59A VAL* 1.3 64.4 + - - +
60A LYS* 3.6 10.2 + - - +
61A ALA* 3.2 22.2 + - - +
62A ALA* 3.2 20.3 + - - +
86A PRO 6.1 0.9 - - - -
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Residues in contact with VAL 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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15A ILE* 3.8 17.9 - - + -
38A TRP* 3.7 32.7 - - + +
58A SER* 1.3 71.0 - - - +
60A LYS* 1.3 63.6 + - - +
62A ALA* 3.1 6.2 + - - +
63A LEU* 2.9 31.7 + - + +
71A PHE* 5.2 1.3 - - + -
82A VAL* 3.7 24.0 - - + -
85A MSE 3.7 27.3 - - + -
88A VAL* 3.6 26.9 - - + -
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Residues in contact with LYS 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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58A SER* 3.3 9.9 + - - +
59A VAL* 1.3 79.5 - - - +
61A ALA* 1.3 62.3 + - - +
63A LEU* 3.5 3.4 + - - +
64A SER* 3.0 31.9 + - - +
86A PRO 4.2 14.8 + - - +
87A GLY* 2.7 46.3 + - - +
88A VAL* 4.1 5.5 - - - +
90A ARG* 3.8 26.1 - - - +
91A ALA* 3.8 19.6 - - + +
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Residues in contact with ALA 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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56A CYS* 4.2 12.1 - - + -
57A GLU* 3.9 23.6 - - + +
58A SER* 3.2 22.5 + - - +
60A LYS* 1.3 76.6 - - - +
62A ALA* 1.3 58.1 + - - +
64A SER* 3.2 7.9 + - - +
65A ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 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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13A SER* 2.5 36.0 + - - -
15A ILE* 4.1 20.0 - - + -
37A ILE* 4.9 0.7 - - - -
38A TRP* 4.2 12.1 - - + +
56A CYS* 3.6 24.0 - - + -
58A SER 3.2 11.4 + - - +
59A VAL 3.1 8.4 + - - +
61A ALA* 1.3 75.9 - - - +
63A LEU* 1.3 61.3 + - - +
65A ALA* 3.3 7.3 + - - -
66A SER 3.8 0.9 + - - -
69A THR* 3.7 1.2 + - - -
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Residues in contact with LEU 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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15A ILE* 4.7 0.9 - - + -
59A VAL* 2.9 24.4 + - + +
60A LYS 3.7 6.3 - - - +
62A ALA* 1.3 74.9 - - - +
64A SER* 1.3 61.2 + - - +
66A SER 3.2 10.6 - - - +
69A THR* 3.4 27.1 + - + +
71A PHE* 4.3 6.1 - - + -
88A VAL* 3.9 21.5 - - + -
91A ALA* 3.7 28.3 - - + +
92A LEU* 3.8 21.1 - - + -
95A ARG* 3.0 26.4 + - + +
97A ILE* 3.5 28.3 - - + -
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Residues in contact with SER 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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7A SER 5.5 0.2 - - - +
8A PHE* 3.6 7.1 - - - -
60A LYS* 3.0 23.0 + - - +
61A ALA* 3.7 6.5 - - - -
63A LEU* 1.3 75.9 - - - +
65A ALA* 1.3 61.9 + - - +
66A SER 3.3 0.9 + - - -
91A ALA* 4.1 12.7 - - - +
95A ARG* 3.3 27.1 + - - +
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Residues in contact with ALA 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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8A PHE* 3.5 10.9 - - - -
9A GLU 4.0 4.0 + - - -
10A PHE* 3.6 39.0 + - + +
13A SER* 4.1 5.6 - - - +
36A ALA* 4.3 7.6 - - + -
54A HIS* 5.8 0.4 - - + -
56A CYS* 4.6 3.8 - - - -
61A ALA 2.9 18.1 + - - +
62A ALA 3.7 7.2 - - - +
63A LEU 3.3 1.2 - - - -
64A SER* 1.3 77.4 - - - +
66A SER* 1.3 58.7 + - - +
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Residues in contact with SER 66 (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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8A PHE* 3.5 6.5 - - - -
10A PHE* 3.4 12.5 - - - +
11A ASP 4.0 0.4 - - - -
12A VAL* 3.1 21.8 + - - -
13A SER* 2.7 25.5 + - - -
62A ALA 3.8 2.4 + - - -
63A LEU 3.2 16.8 - - - +
64A SER 3.3 0.4 - - - -
65A ALA* 1.3 79.3 - - - +
67A PRO* 1.3 76.4 - - - +
68A ALA* 3.4 17.3 + - - -
69A THR* 4.9 0.2 + - - -
95A ARG* 3.4 6.9 + - - -
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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