Contacts of the helix formed by residues 61 - 71 (chain D) in PDB entry 5F28
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 ASP 61 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D ALA* 4.6 1.1 - - - -
60D THR* 1.3 86.4 - - + +
62D MET* 1.3 69.5 + - - +
63D ASP* 3.5 10.6 + - - +
64D LYS* 3.1 50.4 + - + +
65D VAL* 2.9 25.9 + - - +
951E VAL* 5.1 0.5 - - - +
944G PRO* 6.1 1.4 - - - +
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Residues in contact with MET 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C TYR* 3.3 23.1 - - + +
44D ALA* 3.7 22.4 - - - -
45D LEU 4.1 2.5 - - - +
46D ILE* 3.7 27.1 - - + -
56D GLN* 3.9 28.9 - - + +
57D TYR 3.7 24.5 - - - +
58D ALA* 3.9 16.3 - - + +
61D ASP* 1.3 72.6 + - - +
63D ASP* 1.3 56.3 + - - +
65D VAL* 3.1 4.6 + - - +
66D LEU* 2.7 55.9 + - + +
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Residues in contact with ASP 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C TYR* 4.8 4.0 + - - -
61D ASP* 3.4 10.3 + - - +
62D MET* 1.3 80.1 - - - +
64D LYS* 1.3 58.5 + - - +
66D LEU* 3.8 3.8 - - - +
67D LEU* 2.9 30.7 + - - +
951E VAL* 3.6 10.1 - - + +
952E PRO* 3.3 32.0 - - + +
955E LYS* 2.8 40.4 + - + +
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Residues in contact with LYS 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D THR* 5.8 5.6 - - + -
61D ASP* 3.1 35.7 + - + +
63D ASP* 1.3 75.1 - - - +
65D VAL* 1.3 63.7 + - + +
67D LEU* 3.9 3.3 - - + +
68D LYS* 3.1 26.6 + - - +
951E VAL* 3.9 30.3 - - + -
1005E GLN* 5.9 0.9 - - - +
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Residues in contact with VAL 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 4.3 10.3 - - + +
48C PHE* 3.9 21.5 - - + -
42D GLU* 4.6 20.2 - - + +
43D ILE 4.8 9.4 - - - +
44D ALA* 3.8 30.3 - - + +
58D ALA* 5.5 1.1 - - + -
60D THR* 4.3 18.8 - - - +
61D ASP 2.9 23.4 + - - +
62D MET* 3.7 4.0 - - - +
64D LYS* 1.3 74.8 - - + +
66D LEU* 1.3 65.0 + - - +
68D LYS* 3.5 6.7 + - - +
69D TYR* 3.1 20.3 + - - +
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 4.0 24.7 - - + -
66C LEU* 4.0 21.3 - - + -
69C TYR* 3.6 36.1 - - + -
44D ALA* 5.1 2.7 - - + -
46D ILE* 5.4 2.5 - - + -
62D MET* 2.7 41.6 + - + +
63D ASP 3.9 0.2 - - - +
65D VAL* 1.3 71.7 - - - +
67D LEU* 1.3 64.0 + - - +
69D TYR* 3.0 14.8 + - + +
70D THR* 3.1 17.7 + - - +
955E LYS* 3.6 30.3 - - + +
959E LEU* 5.2 8.4 - - + +
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ASP 2.9 19.3 + - - +
64D LYS* 3.9 4.7 - - - +
66D LEU* 1.3 76.6 - - - +
68D LYS* 1.3 63.7 + - - +
69D TYR 3.1 0.2 + - - -
70D THR* 2.7 32.2 + - - +
71D GLU* 3.3 7.3 + - - +
951E VAL* 3.8 20.2 - - + +
954E VAL* 3.8 25.4 - - + +
955E LYS* 3.9 19.9 - - + +
958E GLY* 5.8 0.2 - - - -
994E LEU* 5.9 0.2 - - + -
998E ILE* 4.2 19.7 - - + -
1001E MET* 3.8 31.4 - - + -
1002E LYS* 5.7 3.1 - - - -
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PHE* 3.7 36.8 - - + -
52C ASN* 3.5 28.1 + - + +
42D GLU* 3.1 28.0 + - - +
64D LYS 3.1 16.4 + - - +
65D VAL* 3.8 6.1 - - - +
66D LEU 3.4 0.2 - - - -
67D LEU* 1.3 79.0 - - - +
69D TYR* 1.3 60.2 + - - +
71D GLU* 3.7 20.3 + - - +
72D TYR* 3.8 11.1 + - + +
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Residues in contact with TYR 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ILE* 3.8 29.8 - - + -
48C PHE* 4.0 7.4 - - + -
54C LEU* 3.7 23.1 - - + -
56C GLN* 3.0 31.7 + - - -
62C MET* 3.1 21.9 - - + +
63C ASP* 4.3 2.3 + - - -
66C LEU* 3.6 27.1 - - + -
65D VAL 3.1 12.1 + - - +
66D LEU* 3.0 12.5 + - + +
67D LEU 3.0 1.2 - - - -
68D LYS* 1.3 76.3 - - - +
70D THR* 1.3 71.6 + - + +
71D GLU 3.2 0.4 - - - -
72D TYR* 3.1 15.1 + - - +
959E LEU* 4.9 1.6 - - + -
962E ARG* 3.3 52.5 + - - -
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Residues in contact with THR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LEU 3.4 15.0 - - - +
67D LEU* 2.7 29.6 + - - +
69D TYR* 1.3 79.4 - - + +
71D GLU* 1.3 62.1 + - - +
72D TYR 3.3 1.6 + - - +
955E LYS 3.9 4.7 - - - +
958E GLY* 3.6 24.6 - - - +
959E LEU* 3.5 43.3 - - + +
962E ARG* 4.1 16.7 + - - +
994E LEU* 3.8 13.3 - - - +
998E ILE* 5.0 0.5 - - - +
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Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D LEU* 3.3 7.1 + - - +
68D LYS* 4.0 16.1 - - - +
69D TYR 3.2 0.8 - - - -
70D THR* 1.3 79.1 + - - +
72D TYR* 1.3 62.5 + - - +
73D ASN* 3.2 9.5 + - - +
994E LEU* 4.1 11.5 - - + +
995E GLY* 4.6 12.5 - - - +
998E ILE* 3.7 41.4 - - + +
1002E LYS* 5.0 6.6 + - - -
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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