Contacts of the strand formed by residues 35 - 40 (chain G) in PDB entry 3S4S
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 35 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B VAL* 4.8 11.0 - - + -
162B GLU* 3.3 30.2 + - - +
27G HIS* 3.5 22.6 + - + -
28G TRP 3.7 5.2 - - - +
29G LYS* 3.5 37.9 - - + +
33G GLN 3.5 2.6 + - - +
34G ILE* 1.3 81.0 - - - +
36G ILE* 1.3 59.1 + - - +
45G TRP* 4.2 27.3 - - + -
47G GLY* 3.5 23.8 - - - -
48G PRO* 3.9 3.0 - - + +
49G SER* 4.5 0.2 - - - -
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Residues in contact with ILE 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G TRP* 2.8 16.3 + - + +
29G LYS 3.8 13.9 - - - +
30G ASN* 3.9 5.6 - - + +
34G ILE 3.8 10.3 - - - +
35G LYS* 1.3 72.4 - - - +
37G LEU* 1.3 63.8 + - + +
45G TRP* 4.2 0.4 - - - -
46G LYS* 3.3 7.6 - - - +
47G GLY 3.1 20.8 + - - +
49G SER* 4.1 21.5 - - - +
51G LEU* 4.1 12.1 - - + -
55G ALA* 4.0 26.2 - - + +
69G LEU* 4.1 16.2 - - + -
82G TYR* 3.3 41.1 - - + -
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Residues in contact with LEU 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PHE* 3.8 22.2 - - + -
27G HIS* 3.1 2.8 - - - +
28G TRP* 2.8 42.9 + - + -
36G ILE* 1.3 89.9 - - + +
38G GLY* 1.3 60.4 + - - +
44G LEU* 4.2 13.9 - - + -
45G TRP* 3.2 28.5 - - - +
46G LYS* 4.4 7.2 - - + -
55G ALA* 4.0 8.3 - - + +
56G ASP* 3.5 43.1 - - - +
57G SER* 4.0 6.3 - - - +
68G PRO 4.9 1.1 - - - +
69G LEU* 4.2 10.3 - - + -
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Residues in contact with GLY 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G PHE* 3.2 22.0 - - - -
27G HIS* 3.8 1.3 - - - -
37G LEU* 1.3 84.5 - - - +
39G ASN* 1.3 59.7 + - - -
44G LEU* 3.4 9.3 - - - +
45G TRP* 2.9 41.6 + - - -
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Residues in contact with ASN 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G SER* 4.1 7.7 + - - -
24G ILE 3.8 7.4 + - - -
25G GLN* 3.2 27.6 + - - +
26G PHE* 3.2 48.2 + - - +
38G GLY* 1.3 73.5 - - - -
40G TYR* 1.3 56.8 + - - +
41G GLY 3.6 15.1 + - - +
43G PHE 3.0 16.4 - - - +
45G TRP* 3.4 12.0 + - - -
62G TRP* 3.3 29.7 - - + -
67G PHE* 4.7 0.2 - - - -
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Residues in contact with TYR 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 4.1 13.4 + - - -
104B SER* 3.5 29.6 + - - -
114B LEU* 3.9 16.2 - - + -
116B VAL* 3.6 22.1 - - + +
158B LEU* 4.1 23.8 - - + -
160B MET* 3.6 24.7 - - + -
25G GLN* 4.1 11.2 - - - -
39G ASN* 1.3 73.2 - - - +
41G GLY* 1.3 63.0 + - - +
43G PHE* 2.9 39.0 + + + -
45G TRP* 3.7 18.3 - - + +
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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