Contacts of the strand formed by residues 35 - 42 (chain C) 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 LEU 35 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C THR* 5.2 9.2 - - - -
5C ARG* 3.2 53.2 + - + +
27C CYS* 3.8 27.6 - - + +
28C GLU 3.5 11.2 - - - +
29C GLY* 3.4 37.2 - - - +
33C LYS 3.9 11.4 - - - +
34C ARG* 1.3 79.8 - - - +
36C HIS* 1.3 67.5 + - - +
56C TRP 4.1 4.0 - - - +
57C LEU* 5.2 4.0 - - + -
82C CYS 4.5 0.2 - - - +
83C GLU* 4.2 3.1 - - - +
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Residues in contact with HIS 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ARG* 5.5 0.9 - - - -
7C CYS* 3.6 4.1 - - - -
27C CYS* 4.2 2.1 - - - -
34C ARG* 3.8 14.1 - - + +
35C LEU* 1.3 75.3 - - - +
37C CYS* 1.3 68.8 + - - +
55C CYS* 3.4 6.6 - - - +
56C TRP* 2.9 35.1 + - + +
57C LEU 3.3 24.7 - - - -
58C ASP* 3.5 9.3 - - - -
59C ASP 3.1 22.6 + - - -
62C CYS* 3.1 39.1 - - + +
63C TYR* 3.9 10.0 - + - -
82C CYS 3.1 10.9 + - - +
83C GLU* 3.4 27.6 - - + +
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Residues in contact with CYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ARG* 4.8 2.7 - - - -
6C GLU 3.9 3.4 - - - -
7C CYS* 2.1 48.0 - - - -
36C HIS* 1.3 74.4 - - - +
38C TYR* 1.3 60.9 + - - +
54C GLY 3.3 6.3 - - - -
56C TRP* 4.4 1.6 - - - -
81C CYS* 3.2 8.5 - - - +
82C CYS* 3.0 30.0 + - - -
84C GLY 3.7 11.7 - - - -
87C CYS* 3.4 30.1 - - - -
88C ASN* 3.6 15.9 - - + -
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Residues in contact with TYR 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C CYS* 1.3 75.0 - - - +
39C ALA* 1.3 65.4 + - - +
40C SER* 3.9 10.8 - - - -
52C LYS* 3.2 42.8 - - + +
53C LYS* 3.2 2.9 + - - -
54C GLY* 2.9 53.5 + - - -
55C CYS 3.5 20.4 - - - -
56C TRP* 3.7 14.8 - + + -
68C CYS* 4.5 0.7 - - - -
79C PHE* 3.7 27.4 - + + -
80C CYS 3.2 14.8 - - - +
81C CYS* 4.2 0.4 - - - +
88C ASN* 2.6 29.8 + - - -
92D LEU* 4.7 6.3 - - + -
102D LYS* 3.3 32.7 - - + +
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C TYR* 1.3 78.6 - - - +
40C SER* 1.3 63.0 + - - +
41C TRP* 4.0 3.8 - - + -
52C LYS 3.4 7.4 - - - -
53C LYS* 4.2 13.7 - - + -
68C CYS* 4.0 3.8 - - - -
79C PHE* 3.3 5.5 - - - -
80C CYS* 3.0 47.6 + - - +
88C ASN* 4.5 4.0 - - + -
91C PHE* 4.2 20.2 - - + -
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C TYR* 3.9 2.5 - - - -
39C ALA* 1.3 77.6 - - - +
41C TRP* 1.3 67.7 + - - +
50C LEU* 3.9 4.9 - - - +
51C VAL* 2.9 26.0 + - - +
52C LYS* 2.8 35.4 + - - +
77C VAL* 4.3 6.1 - - - -
78C TYR 3.1 14.1 - - - -
79C PHE* 4.5 0.2 - - - -
92D LEU* 3.6 29.1 - - - +
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Residues in contact with TRP 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ALA* 4.0 6.3 - - + -
40C SER* 1.3 89.7 - - - +
42C ARG* 1.3 85.7 + - - +
43C ASN* 4.3 3.4 - - + +
48C ILE* 4.1 19.7 - - + +
49C GLU 3.3 12.8 - - - +
50C LEU* 4.1 7.2 - - + -
51C VAL* 3.9 7.3 - - - +
70C ALA* 3.7 12.1 - - + -
77C VAL* 3.7 3.7 - - - +
78C TYR* 2.9 67.1 + + + -
80C CYS* 3.7 23.1 - - + -
91C PHE* 3.3 47.3 - + + -
92C THR* 3.5 29.6 - - - -
93C HIS* 4.6 2.0 - - + -
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C TRP* 1.3 86.4 - - - +
43C ASN* 1.3 64.5 + - - +
44C SER* 5.1 2.7 - - - +
47C THR 4.6 0.2 - - - -
48C ILE* 3.5 0.5 - - - -
49C GLU* 2.7 66.7 + - + +
51C VAL* 3.6 8.6 - - + +
76C GLN* 3.8 19.1 + - - +
77C VAL* 4.3 6.7 - - + +
78C TYR* 4.4 0.9 - - - -
94D TYR* 3.7 27.9 + - - -
98D GLN 5.4 2.6 + - - -
100D ILE* 3.3 29.0 - - - +
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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