Contacts of the strand formed by residues 36 - 43 (chain A) in PDB entry 3I85
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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ASP* 4.4 0.2 - - - +
33A LEU* 2.7 46.8 + - + +
35A SER* 1.3 92.3 - - - +
37A ILE* 1.3 60.7 + - - +
75A LYS* 3.9 37.5 - - + +
76A VAL 3.2 9.0 - - - +
77A ASP* 3.3 28.5 + - - +
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Residues in contact with ILE 37 (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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30A VAL* 4.0 15.9 - - + -
31A GLU 3.6 7.2 - - - +
32A ASP* 4.0 29.4 - - - +
33A LEU* 4.4 1.6 - - - -
35A SER 5.4 0.4 - - - -
36A LYS* 1.3 78.2 - - - +
38A LEU* 1.3 62.3 + - - +
39A LEU* 3.5 25.1 + - + -
74A PHE 3.6 1.0 - - - +
75A LYS* 3.4 1.9 - - - -
76A VAL* 2.6 46.6 + - + +
81A GLN* 3.0 33.7 - - + +
101B LEU* 4.2 14.4 - - + -
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Residues in contact with LEU 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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29A THR 3.6 0.9 - - - +
30A VAL* 3.2 5.0 - - - -
31A GLU* 2.9 63.2 + - + +
33A LEU* 3.2 24.7 - - + +
37A ILE* 1.3 72.4 - - - +
39A LEU* 1.3 65.0 + - - +
40A THR* 3.9 14.8 + - - +
73A GLU* 3.8 34.3 - - + +
74A PHE 3.7 19.3 - - - +
75A LYS* 3.9 17.7 - - + +
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Residues in contact with LEU 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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29A THR 3.4 3.1 - - - -
30A VAL* 3.7 17.9 - - + -
37A ILE* 3.5 26.0 - - + -
38A LEU* 1.3 72.1 - - - +
40A THR* 1.3 62.6 + - - +
55A TRP* 4.0 15.6 - - + -
73A GLU* 3.2 4.3 - - - +
74A PHE* 2.7 49.1 + - + +
76A VAL* 4.0 9.9 - - + -
85A TYR* 3.6 44.2 - - + -
99B ILE* 3.7 15.0 - - + -
101B LEU* 3.9 15.7 - - + -
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Residues in contact with THR 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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27A PHE 4.4 0.4 - - - -
28A THR* 3.4 5.4 - - - -
29A THR* 2.7 52.3 + - - +
31A GLU* 5.1 2.9 + - - +
38A LEU* 3.9 18.7 + - - +
39A LEU* 1.3 79.7 + - - +
41A CYS* 1.3 70.2 + - - +
42A SER* 4.3 2.2 - - - +
55A TRP* 4.6 0.4 - - - -
71A LYS* 3.5 42.0 - - + -
72A THR 3.4 6.1 - - - +
73A GLU* 4.1 10.2 - - + +
99B ILE* 4.0 1.8 - - - +
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Residues in contact with CYS 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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26A VAL* 4.0 2.2 - - + -
27A PHE 3.3 2.9 - - - -
28A THR* 3.7 15.9 - - - -
40A THR* 1.3 77.3 - - - +
42A SER* 1.3 63.8 + - - +
55A TRP* 3.7 11.0 - - - -
71A LYS* 3.2 5.7 - - - +
72A THR* 2.8 49.7 + - + -
87A CYS* 2.0 50.5 - - - -
89A PHE* 3.6 8.5 - - + -
99B ILE* 4.6 0.9 - - - -
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Residues in contact with SER 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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25A THR 3.7 0.9 - - - +
26A VAL* 3.2 6.3 - - - -
27A PHE* 2.6 53.7 + - - +
29A THR* 5.6 1.7 + - - -
40A THR* 4.3 2.6 - - - +
41A CYS* 1.3 76.2 + - - +
43A LEU* 1.3 63.4 + - - +
44A ASP 3.8 0.3 + - - -
70A GLN* 3.2 6.5 - - - -
71A LYS* 3.7 24.2 - - - +
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Residues in contact with LEU 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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24A GLY* 4.7 7.6 - - - -
25A THR 4.0 10.1 - - - +
26A VAL* 4.2 18.4 - - + +
42A SER* 1.3 73.8 - - - +
44A ASP* 1.3 65.0 + - - +
45A ASP 3.4 11.9 + - - +
48A THR 5.0 2.2 - - - +
50A VAL* 3.6 21.8 - - + -
70A GLN* 2.5 48.1 + - - +
89A PHE* 3.7 27.0 - - + -
94B MET* 4.2 20.0 - - + +
95B GLY* 4.4 12.3 - - - +
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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