Contacts of the strand formed by residues 35 - 44 (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 LEU 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ARG* 2.8 65.6 + - + +
27A CYS* 3.6 27.8 - - + +
28A GLU 4.0 15.0 - - - +
29A GLY* 4.5 18.2 - - - +
33A LYS 4.0 7.6 + - - +
34A ARG* 1.3 78.1 - - - +
36A HIS* 1.3 74.1 + - - +
55A CYS* 5.8 0.4 - - + -
56A TRP 4.1 9.4 - - - +
57A LEU* 4.9 9.6 - - + -
83A GLU* 3.5 1.6 - - - +
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Residues in contact with HIS 36 (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* 4.3 2.9 - - - +
7A CYS* 3.6 4.8 - - - -
27A CYS* 4.2 2.1 - - - -
34A ARG* 3.8 13.7 - - + +
35A LEU* 1.3 83.0 - - - +
37A CYS* 1.3 66.8 + - - +
55A CYS* 3.6 6.1 - - - +
56A TRP* 3.0 37.2 + - + +
57A LEU 3.5 8.9 + - - -
58A ASP* 3.5 10.1 - - - -
59A ASP 3.2 43.0 + - - -
62A CYS* 3.4 26.2 - - + +
63A TYR* 3.8 17.7 - + - -
82A CYS 3.2 13.5 - - - +
83A GLU* 3.6 18.9 - - + +
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Residues in contact with CYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 4.4 1.6 - - - -
6A GLU 3.8 4.0 - - - -
7A CYS* 2.1 45.8 - - - -
36A HIS* 1.3 74.1 - - - +
38A TYR* 1.3 61.1 + - - +
54A GLY 3.2 6.5 - - - +
56A TRP* 4.1 2.7 - - - -
81A CYS* 3.1 7.6 - - - +
82A CYS* 3.0 31.0 + - - +
84A GLY 3.7 21.8 - - - -
86A PHE 4.2 2.2 - - - -
87A CYS* 4.0 7.6 - - - -
88A ASN* 3.4 26.9 - - + -
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Residues in contact with TYR 38 (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* 1.3 76.0 - - - +
39A ALA* 1.3 67.7 + - - +
40A SER* 4.0 10.1 - - - -
52A LYS* 3.3 35.6 - - + +
53A LYS* 3.4 4.2 + - - -
54A GLY* 2.8 46.0 + - - -
55A CYS 3.4 21.1 - - - -
56A TRP* 3.6 13.9 - + + -
68A CYS* 4.8 0.2 - - - -
79A PHE* 3.7 28.5 - + + -
80A CYS 3.0 13.0 - - - +
81A CYS* 4.1 0.4 - - + +
88A ASN* 2.9 24.4 + - - -
92B LEU* 4.4 10.1 - - + -
102B LYS* 3.4 33.4 - - + +
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Residues in contact with ALA 39 (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* 1.3 82.1 - - - +
40A SER* 1.3 65.7 + - - +
41A TRP* 4.4 1.6 - - + -
52A LYS 3.5 7.2 - - - -
53A LYS* 3.8 15.9 - - + -
68A CYS* 4.3 2.9 - - - -
79A PHE* 3.4 1.7 - - - -
80A CYS* 2.7 41.7 + - - +
88A ASN* 4.5 4.9 - - + +
91A PHE* 3.8 29.8 - - + -
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Residues in contact with SER 40 (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* 4.0 2.4 - - - -
39A ALA* 1.3 79.0 - - - +
41A TRP* 1.3 66.1 + - - +
50A LEU* 3.7 6.8 - - - +
51A VAL* 2.9 29.6 + - - +
52A LYS* 2.9 35.9 + - - +
77A VAL* 4.6 3.1 - - - -
78A TYR 3.0 16.6 - - - -
79A PHE* 4.6 0.7 - - - -
92B LEU* 3.8 26.0 - - - +
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Residues in contact with TRP 41 (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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40A SER* 1.3 85.6 - - - +
42A ARG* 1.3 85.7 - - - +
43A ASN* 4.2 0.4 - - + -
48A ILE* 3.8 22.6 - - + +
49A GLU 3.5 13.0 - - - +
50A LEU* 4.2 3.6 - - + -
51A VAL* 4.0 7.2 - - - +
70A ALA* 3.9 12.6 - - + -
77A VAL* 3.6 3.8 - - - +
78A TYR* 2.8 49.6 + + + -
80A CYS* 3.9 22.9 - - - -
91A PHE* 3.4 52.2 - + + -
92A THR 3.6 17.3 - - - -
93A HIS* 2.9 49.0 + + - -
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Residues in contact with ARG 42 (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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41A TRP* 1.3 87.7 - - - +
43A ASN* 1.3 62.3 + - - +
44A SER* 4.1 7.4 - - - +
47A THR 4.7 0.2 - - - -
48A ILE* 3.6 0.7 - - - -
49A GLU* 2.6 82.4 + - + +
51A VAL* 3.7 14.9 - - + +
76A GLN* 3.8 34.1 - - - +
77A VAL* 4.0 10.7 - - + +
94B TYR* 4.9 4.4 + - - -
100B ILE* 3.6 27.1 - - - +
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Residues in contact with ASN 43 (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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41A TRP* 4.3 2.7 - - + +
42A ARG* 1.3 73.8 - - - +
44A SER* 1.3 63.8 + - - +
45A SER* 3.8 2.6 + - - -
46A GLY* 3.2 26.0 + - - +
47A THR 3.5 12.9 + - - -
48A ILE* 4.9 5.7 - - + +
76A GLN 4.7 1.6 + - - -
78A TYR* 3.7 30.6 + - + +
93A HIS* 3.0 31.3 + - + +
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Residues in contact with SER 44 (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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42A ARG* 5.3 7.2 - - - -
43A ASN* 1.3 76.1 + - - +
45A SER* 1.3 71.3 + - - +
46A GLY 3.5 0.2 - - - -
47A THR* 3.3 27.1 + - - -
49A GLU* 6.4 1.8 - - - -
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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