Contacts of the helix formed by residues 63 - 69 (chain D) in PDB entry 1S77
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 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D ARG* 4.2 8.3 + - - -
58D GLN* 3.0 43.7 + - - +
59D LEU* 4.3 0.6 - - - +
61D ALA* 3.7 9.9 - - - +
62D GLY* 1.3 82.2 - - - +
64D VAL* 1.3 69.6 + - - +
65D ALA* 3.4 2.7 - - - +
66D ASP* 3.3 34.8 + - + +
67D ASN 3.9 1.6 + - - -
120D LYS* 5.4 9.9 - - - +
124D ALA* 4.6 4.4 - - - +
176D HIS* 4.5 18.0 + - + +
111T T 4.9 7.7 + - - -
112T G 4.6 14.5 + - - +
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Residues in contact with VAL 64 (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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55D PHE* 4.8 11.2 - - + -
58D GLN* 5.1 1.3 - - - -
59D LEU* 3.2 31.0 - - + +
63D GLU* 1.3 72.4 - - - +
65D ALA* 1.3 56.5 + - - +
66D ASP 2.6 17.0 + - - -
67D ASN* 2.7 25.3 + - + +
70D ALA* 3.8 16.2 - - + +
123D LEU* 5.1 7.0 - - + +
124D ALA* 5.3 2.6 - - - +
127D THR* 2.8 42.3 + - + +
254D ILE* 4.2 24.7 - - + -
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Residues in contact with ALA 65 (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 GLU* 3.4 1.1 - - - -
64D VAL* 1.3 77.9 - - - +
66D ASP* 1.3 63.1 + - - +
67D ASN 3.8 5.1 - - - +
70D ALA* 4.1 8.6 - - - +
71D LYS* 4.4 4.5 + - - +
74D ILE* 3.3 37.2 - - + +
116D TYR* 5.1 2.2 + - - +
119D ILE 5.2 0.9 - - - +
120D LYS* 3.8 41.3 - - + +
123D LEU* 5.2 11.3 - - + +
124D ALA* 5.9 1.4 - - + +
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Residues in contact with ASP 66 (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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58D GLN* 4.7 9.3 + - - +
63D GLU* 3.3 41.9 - - - +
64D VAL 2.6 4.9 + - - -
65D ALA* 1.3 74.4 - - - +
67D ASN* 1.3 66.0 + - - +
68D ALA* 3.4 2.3 + - - -
71D LYS* 5.2 4.2 - - - +
116D TYR* 4.1 9.1 + - - -
120D LYS* 3.7 22.7 + - - -
752D LEU 4.4 2.3 - - - +
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Residues in contact with ASN 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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51D PHE* 3.9 9.7 - - - -
54D MET* 3.1 34.6 - - - +
55D PHE* 3.2 34.7 - - + +
58D GLN* 4.5 14.7 - - + +
63D GLU 3.9 1.0 + - - -
64D VAL* 2.7 22.6 + - + +
65D ALA 3.8 0.2 - - - +
66D ASP* 1.3 77.7 - - - +
68D ALA* 1.3 70.8 + - - +
69D ALA* 2.7 35.0 + - + +
70D ALA 3.0 13.4 + - - +
71D LYS* 3.4 5.9 + - - +
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Residues in contact with ALA 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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51D PHE* 5.6 2.7 - - + -
66D ASP 3.4 3.1 + - - -
67D ASN* 1.3 74.5 + - - +
69D ALA* 1.3 64.7 + - - +
71D LYS* 2.9 23.7 + - - +
72D PRO* 2.9 12.0 - - - +
257D ARG* 4.4 4.0 + - - +
261D LEU* 3.2 24.9 - - + -
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Residues in contact with ALA 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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55D PHE* 4.1 8.1 - - + -
67D ASN* 2.7 22.2 + - + +
68D ALA* 1.3 72.4 - - - +
70D ALA* 1.3 55.6 + - - +
72D PRO* 3.5 7.6 - - - +
73D LEU* 4.9 1.0 + - - +
254D ILE* 3.4 35.4 - - + +
257D ARG* 3.0 34.9 - - + +
258D ALA* 3.8 15.3 - - - +
261D LEU* 3.5 3.4 - - + +
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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