Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 1S4Y
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 TYR 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A SER* 3.0 28.2 - - - -
41A TRP* 2.8 48.9 + + + +
42A ARG* 4.4 0.7 - - - -
43A ASN* 3.7 33.6 + - + +
70A ALA* 4.1 4.3 - - + -
72A GLU 3.7 11.0 - - - -
73A GLU 3.5 19.2 + - - -
74A ASN* 3.6 15.9 + - - -
75A PRO* 3.1 40.7 + - + -
76A GLN 4.8 0.9 - - - -
77A VAL* 1.3 75.8 - - - +
79A PHE* 1.3 61.0 - - - +
93A HIS* 3.7 31.3 - + - -
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Residues in contact with PHE 79 (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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38A TYR* 3.7 27.6 - + + -
39A ALA 3.4 9.9 - - - -
40A SER* 4.9 0.2 - - - -
41A TRP* 4.5 1.1 - - - -
56A TRP* 3.6 49.4 - + - -
59A ASP* 5.6 2.0 - - - -
61A ASN* 6.0 2.2 - - + -
70A ALA* 3.4 4.0 - - - +
71A THR* 3.0 47.9 + - + +
77A VAL 4.1 0.2 + - - -
78A TYR* 1.3 75.7 - - - +
80A CYS* 1.3 72.7 + - - +
81A CYS* 3.9 16.8 - - + -
30B ILE* 4.8 10.3 - - + +
31B ALA* 3.6 26.2 - - + -
32B PRO* 6.0 1.3 - - + -
92B LEU* 4.1 10.1 - - + -
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Residues in contact with CYS 80 (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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38A TYR* 3.0 7.4 - - - +
39A ALA* 2.7 47.3 + - - +
41A TRP* 3.9 5.2 - - + -
68A CYS* 2.1 48.5 - - - -
69A VAL 3.2 32.5 - - - +
70A ALA* 3.7 1.8 - - - +
71A THR* 5.0 1.3 - - - +
79A PHE* 1.3 80.7 - - - +
81A CYS* 1.3 60.0 + - - +
91A PHE* 3.7 15.9 - - - -
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Residues in contact with CYS 81 (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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37A CYS 3.1 15.7 - - - +
38A TYR* 4.2 1.6 - - + -
56A TRP* 4.6 1.6 - - + -
61A ASN* 4.1 9.4 - - - -
62A CYS* 2.1 56.3 - - - -
65A ARG* 4.3 10.6 + - - +
67A GLU 3.8 9.0 - - - +
68A CYS* 3.8 4.5 - - - -
69A VAL 4.8 2.3 + - - +
71A THR* 5.6 4.1 - - - +
79A PHE* 3.9 22.4 - - + -
80A CYS* 1.3 76.1 - - - +
82A CYS* 1.3 65.3 + - - +
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Residues in contact with CYS 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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36A HIS* 3.2 14.1 - - - +
37A CYS* 3.0 33.8 + - - -
62A CYS 4.4 2.5 - - - -
65A ARG* 3.8 7.2 - - - +
66A GLN 3.9 2.5 - - - +
67A GLU 3.5 25.4 - - - +
68A CYS* 3.9 8.5 - - - +
81A CYS* 1.3 79.0 - - - +
83A GLU* 1.3 57.0 + - - +
87A CYS* 2.1 59.5 - - + -
88A ASN 3.5 3.1 - - - -
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Residues in contact with GLU 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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5A ARG* 3.5 19.9 + - - +
34A ARG* 3.2 39.5 + - - +
35A LEU 3.5 9.4 - - - +
36A HIS* 3.6 9.6 - - + +
62A CYS 4.2 3.5 + - - +
63A TYR* 3.8 3.3 - - - -
64A ASP* 3.0 29.0 + - - +
65A ARG 2.7 25.2 + - - +
66A GLN* 4.1 6.9 - - - +
82A CYS* 1.3 71.2 - - - +
84A GLY* 1.3 61.2 + - - +
87A CYS* 3.4 14.6 - - - +
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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