Contacts of the strand formed by residues 81 - 89 (chain A) in PDB entry 1SY2
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 LYS 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ASN* 3.2 18.3 + - - +
6A ALA 2.7 32.2 + - - +
7A ILE* 5.3 0.9 - - + -
8A ALA* 4.2 10.3 - - + +
77A GLU* 2.9 34.8 + - + -
78A SER* 3.0 31.4 + - - +
79A LEU 3.3 0.2 - - - -
80A GLY* 1.3 77.5 - - - +
82A TYR* 1.3 65.1 + - - +
107A PHE 3.4 2.9 - - - -
108A THR* 3.0 35.0 + - + +
120A HIS* 6.0 0.2 + - - -
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Residues in contact with TYR 82 (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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12A PHE* 3.5 15.0 - + - -
14A LYS* 4.4 7.6 - - - +
18A PHE* 3.7 28.0 - + - -
53A LEU* 3.7 26.2 - - + -
74A LEU* 3.7 24.2 - - + -
75A GLN 3.2 14.4 - - - +
76A VAL* 3.9 21.1 - - + -
77A GLU* 4.4 3.5 - - - +
78A SER 4.5 0.2 + - - -
79A LEU* 4.4 3.3 - - - +
80A GLY* 3.2 38.6 + - - -
81A LYS* 1.3 80.1 - - - +
83A THR* 1.3 63.0 + - - +
106A THR* 3.3 8.1 - - - -
107A PHE* 2.8 47.3 + + + +
109A VAL* 4.9 3.8 - - + -
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Residues in contact with THR 83 (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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74A LEU* 3.6 1.5 - - - -
75A GLN* 2.9 44.6 + - - +
77A GLU* 2.6 32.0 + - - +
82A TYR* 1.3 73.9 + - - +
84A ALA* 1.3 61.3 + - - +
85A ASN* 4.2 9.6 - - - +
104A TYR* 3.7 32.8 - - + -
105A TYR 3.6 3.1 - - - -
106A THR* 4.4 8.4 - - - +
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Residues in contact with ALA 84 (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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72A SER* 3.8 6.1 - - - -
74A LEU* 3.7 23.6 - - + +
83A THR* 1.3 74.3 - - - +
85A ASN* 1.3 61.9 + - - +
86A PHE 3.5 1.6 + - - -
104A TYR* 3.1 5.4 - - - -
105A TYR* 2.8 75.0 + - + +
107A PHE* 5.6 1.1 - - + -
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Residues in contact with ASN 85 (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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72A SER* 3.4 15.2 + - - -
73A GLU 4.4 8.2 + - - +
75A GLN* 3.6 22.9 - - - +
83A THR* 4.2 6.9 + - - +
84A ALA* 1.3 69.0 - - - +
86A PHE* 1.3 60.9 + - - +
99A VAL* 4.0 28.1 - - + +
100A THR 3.7 11.4 - - - +
101A ALA* 4.7 4.9 - - - -
102A GLY 4.7 0.3 + - - -
103A ASN 3.2 17.4 + - - +
104A TYR* 3.5 16.1 - - - +
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Residues in contact with PHE 86 (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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70A ASP* 3.6 13.5 - - + +
71A VAL 3.6 1.1 - - - +
72A SER* 3.2 17.7 - - - +
85A ASN* 1.3 72.8 - - - +
87A LYS* 1.3 60.0 + - - +
88A LYS 5.0 0.4 - - - -
98A ALA 4.3 2.4 - - - +
99A VAL* 3.8 16.2 - - - -
103A ASN* 3.5 43.7 + - + +
104A TYR* 3.3 29.8 - - - -
105A TYR* 3.9 7.4 - + + -
123A LEU* 3.6 27.1 - - + -
124A HIS 3.9 2.5 - - - -
125A LYS* 4.2 5.4 - - + -
185A HEM 3.5 57.2 - - + -
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Residues in contact with LYS 87 (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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70A ASP* 3.2 6.1 - - - -
71A VAL* 2.9 65.2 + - + +
86A PHE* 1.3 75.2 - - - +
88A LYS* 1.3 62.7 + - - +
89A VAL* 3.6 7.9 + - + +
93A GLY 5.5 0.2 + - - -
95A VAL* 3.9 25.8 - - + +
97A VAL 3.3 14.8 - - - +
98A ALA* 4.1 1.3 - - - -
99A VAL* 3.8 24.0 - - + +
184A LYS* 2.9 26.1 + - - -
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Residues in contact with LYS 88 (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 PHE* 3.9 29.2 - - + +
69A TYR 3.5 13.5 - - - +
70A ASP* 3.5 3.2 + - - -
86A PHE* 4.3 1.2 - - - -
87A LYS* 1.3 73.1 - - - +
89A VAL* 1.3 62.8 + - - +
95A VAL* 3.8 1.0 - - - -
96A LYS* 2.8 46.6 + - + +
97A VAL* 3.0 40.6 + - + +
125A LYS* 4.4 8.1 - - - +
185A HEM 3.4 34.6 + - - +
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Residues in contact with VAL 89 (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 PHE* 5.3 0.2 - - - -
69A TYR* 3.0 39.5 + - + +
70A ASP* 4.1 11.2 - - - +
71A VAL* 3.7 22.2 - - + -
87A LYS* 3.9 11.4 - - + +
88A LYS* 1.3 80.7 - - - +
90A ASP* 1.3 74.3 + - - +
93A GLY 3.7 20.0 - - - +
94A ASN 3.1 10.5 - - - +
95A VAL* 4.1 4.9 - - - -
96A LYS* 4.0 10.3 - - - +
181A LEU* 3.9 17.9 - - + -
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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