Contacts of the helix formed by residues 59 - 65 (chain A) in PDB entry 1S3Y
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 ARG 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A GLY* 1.3 71.3 - - - -
60A LYS* 1.3 64.7 + - + +
62A TRP* 2.9 18.5 + - + +
63A GLU* 3.1 38.3 + - + +
79A VAL* 3.9 15.9 - - + -
80A ILE 3.6 10.3 + - - +
81A THR* 4.1 7.9 - - + -
83A ASN* 3.7 25.6 + - - +
85A SER* 6.1 1.6 - - - +
86A LEU* 5.3 10.7 - - - +
87A ASP* 5.9 1.7 + - - -
207A NAP 3.3 48.8 + - - +
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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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23A ASN* 4.2 15.8 + - - +
59A ARG* 1.3 77.7 - - + +
61A THR* 1.3 55.6 + - - +
63A GLU* 3.2 20.4 + - - +
64A SER* 2.9 28.5 + - - -
207A NAP 3.0 76.5 + - + +
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Residues in contact with THR 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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57A MET* 3.9 26.0 - - + -
58A GLY 3.1 9.8 + - - -
60A LYS* 1.3 75.7 - - - +
62A TRP* 1.3 64.3 + - - +
64A SER* 3.0 14.9 + - - -
65A ILE* 3.3 21.3 + - + +
123A ILE* 4.8 5.8 - - + -
124A GLY* 4.1 6.1 - - - -
125A GLY 3.2 12.8 + - - -
207A NAP 2.8 58.2 + - + -
208A TQT 5.4 2.0 - - + -
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Residues in contact with TRP 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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57A MET* 3.7 19.9 - - + -
58A GLY 3.1 5.3 + - - +
59A ARG* 2.9 16.2 + - + +
61A THR* 1.3 79.8 - - - +
63A GLU* 1.3 63.9 + - + +
65A ILE* 3.6 5.6 + - + +
70A ARG* 3.0 84.4 + - + +
71A PRO* 3.8 13.0 - - + -
77A ASN* 3.9 21.5 - - + -
79A VAL* 3.4 36.3 - - + -
89A GLY* 5.3 7.0 - - - -
92A ILE* 3.4 36.6 - - + -
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Residues in contact with GLU 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 ARG* 3.1 36.3 + - + +
60A LYS* 3.6 29.5 + - - +
61A THR 3.1 0.2 - - - -
62A TRP* 1.3 80.8 - - + +
64A SER* 1.3 58.0 + - - +
65A ILE 2.9 19.0 + - - +
70A ARG* 3.7 13.1 + - - +
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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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23A ASN 5.2 1.2 + - - -
25A LEU* 5.4 2.6 - - - +
60A LYS 2.9 13.5 + - - -
61A THR* 3.0 15.2 + - - -
63A GLU* 1.3 75.6 - - - +
65A ILE* 1.3 59.9 + - - +
66A PRO* 3.6 3.8 - - - +
207A NAP 4.0 33.1 + - - -
208A TQT 3.4 27.5 - - - -
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Residues in contact with ILE 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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57A MET* 4.3 22.4 - - + -
61A THR* 3.4 21.5 - - + +
62A TRP* 3.9 7.2 - - + +
63A GLU 2.9 2.6 + - - +
64A SER* 1.3 81.1 - - - +
66A PRO* 1.3 71.4 - - + +
69A PHE* 4.2 19.5 - - + +
70A ARG* 2.6 56.0 + - + -
72A LEU* 4.7 14.8 - - + -
123A ILE* 5.2 1.8 - - + -
208A TQT 4.1 36.1 - - + +
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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