Contacts of the helix formed by residues 65 - 73 (chain A) in PDB entry 1SA4
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 LEU 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TYR* 4.1 10.7 - - + -
64A VAL* 1.3 84.7 - - - +
66A TYR* 1.3 60.6 + - - +
67A ARG* 3.1 45.3 - - + +
68A ASP* 2.9 33.3 + - - +
69A ARG* 3.3 2.4 - - - +
94A ASP* 3.4 9.9 - - - +
95A LYS* 3.7 37.0 - - + +
98A ASP* 3.5 16.8 - - - +
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Residues in contact with TYR 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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63A TYR* 3.5 19.7 - - - -
65A LEU* 1.3 71.7 - - - +
67A ARG* 1.3 59.6 + - - +
68A ASP 2.9 1.6 + - - -
69A ARG* 3.1 43.7 + - - +
72A TRP* 3.4 60.0 - + + +
98A ASP* 2.7 22.3 + - - +
99A VAL* 3.8 10.5 - - + -
102A TYR* 3.6 26.0 + + + -
118A LYS* 4.2 3.3 + - - +
119A LEU* 3.5 39.4 + - + -
122A ASP* 2.5 27.7 + - - -
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Residues in contact with ARG 67 (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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65A LEU* 3.1 27.0 - - + +
66A TYR* 1.3 76.8 - - - +
68A ASP* 1.3 73.5 + - - +
69A ARG 3.6 1.2 - - - +
77A PRO* 6.1 0.9 - - + -
94A ASP* 2.7 42.0 + - - -
98A ASP* 3.1 24.0 + - - +
102A TYR* 3.3 22.5 + - + +
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Residues in contact with ASP 68 (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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64A VAL* 3.6 16.4 - - + +
65A LEU* 2.9 31.0 + - - +
67A ARG* 1.3 97.3 + - - +
69A ARG* 1.3 60.8 + - - +
70A ALA 3.7 2.1 + - - -
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Residues in contact with ARG 69 (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 VAL* 4.0 18.8 - - - +
63A TYR* 3.2 30.5 - - - -
64A VAL* 2.8 37.7 + - + +
65A LEU 3.3 13.4 + - - +
66A TYR* 3.1 41.1 + - - +
67A ARG 3.6 1.4 - - - +
68A ASP* 1.3 77.1 - - - +
70A ALA* 1.3 66.3 + - - +
71A GLU* 3.6 29.0 + - - +
72A TRP* 3.0 32.2 + - + +
73A ALA* 3.3 10.0 + - - +
122A ASP* 4.4 1.4 + - - -
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Residues in contact with ALA 70 (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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68A ASP 3.7 4.2 + - - -
69A ARG* 1.3 72.5 - - - +
71A GLU* 1.3 62.5 + - - +
72A TRP 3.0 4.6 + - - -
73A ALA* 3.2 22.6 + - - +
74A ASP* 4.8 0.5 + - - +
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Residues in contact with GLU 71 (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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69A ARG* 3.6 29.1 + - - +
70A ALA* 1.3 82.3 + - - +
72A TRP* 1.3 66.2 + - + +
73A ALA 3.6 0.4 - - - -
74A ASP* 3.6 3.7 - - - +
115A ARG* 2.7 34.0 + - + -
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Residues in contact with TRP 72 (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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66A TYR* 3.4 49.4 - + - +
69A ARG* 3.0 22.7 + - + +
70A ALA 3.0 1.0 - - - -
71A GLU* 1.3 102.4 + - + +
73A ALA* 1.3 64.2 + - - +
74A ASP* 3.2 5.2 + - - -
75A ILE* 3.3 45.1 + - + +
102A TYR* 3.8 19.8 + + + -
106A VAL* 3.6 25.8 - - + -
115A ARG* 3.2 68.1 - - + +
116A ALA 4.1 0.2 - - - -
119A LEU* 3.8 20.4 - - + -
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Residues in contact with ALA 73 (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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69A ARG 3.3 6.2 + - - +
70A ALA* 3.2 22.0 + - + +
71A GLU 3.6 0.2 - - - -
72A TRP* 1.3 78.4 - - - +
74A ASP* 1.3 61.7 + - - +
75A ILE 3.3 4.6 + - - +
76A ASP* 5.4 2.1 - - - +
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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