Contacts of the strand formed by residues 35 - 40 (chain H) in PDB entry 4R2G
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H HIS* 4.6 13.9 - - + +
28H TRP 3.9 6.1 - - - +
29H LYS* 4.4 8.3 - - + -
33H GLN 3.6 0.4 + - - +
34H ILE* 1.3 73.7 - - - +
36H ILE* 1.3 59.5 + - - +
37H LEU 4.9 3.8 - - - +
47H GLY* 3.4 17.5 - - - -
48H PRO* 3.7 13.3 - - + +
49H SER* 3.2 26.2 + - - -
280K ASN* 3.6 28.7 + - - +
281K ALA* 4.4 12.0 - - - +
455K THR* 3.6 27.3 + - - +
456K ARG 2.9 29.4 + - - -
457K ASP* 4.0 15.7 + - - +
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Residues in contact with ILE 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H TRP* 2.9 20.0 + - + +
29H LYS 4.0 17.7 - - - -
30H ASN* 4.1 8.3 - - + +
34H ILE 4.2 0.4 - - - +
35H LYS* 1.3 74.5 - - - +
37H LEU* 1.3 62.7 + - + +
46H LYS* 3.8 4.9 - - - +
47H GLY 3.0 23.6 + - - +
49H SER* 3.7 23.0 + - - +
51H LEU* 3.3 31.2 - - + -
52H ASN* 4.7 1.4 - - - +
55H ALA* 4.2 13.9 - - + +
69H LEU* 3.6 30.7 - - + -
82H TYR* 3.5 17.7 - - + -
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Residues in contact with LEU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H PHE* 3.6 29.2 - - + -
27H HIS* 3.6 10.5 - - - -
28H TRP* 3.2 31.6 + - + +
35H LYS* 3.8 1.6 - - - +
36H ILE* 1.3 87.0 + - + +
38H GLY* 1.3 73.4 + - - +
44H LEU* 4.0 17.9 - - + -
45H THR* 3.4 12.8 - - - +
46H LYS* 4.4 5.8 - - + +
47H GLY* 4.0 2.2 - - - +
55H ALA* 4.2 5.8 - - + -
56H ASP* 3.5 44.4 - - - +
57H SER* 4.2 7.9 - - - +
68H PRO 4.7 1.6 - - - +
69H LEU* 3.7 13.5 - - + -
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Residues in contact with GLY 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H PHE* 3.6 19.9 - - - -
27H HIS* 4.1 6.7 - - - -
37H LEU* 1.3 84.8 - - - +
39H ASN* 1.3 61.1 + - - +
44H LEU* 3.2 13.7 - - - +
45H THR* 2.9 32.4 + - - -
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Residues in contact with ASN 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H SER* 4.9 3.0 + - - -
24H ILE 3.3 23.4 + - - -
25H GLN* 3.1 13.3 + - - +
26H PHE* 2.8 48.5 + - + +
27H HIS* 3.5 4.6 - - - -
38H GLY* 1.3 75.9 - - - +
40H GLN* 1.3 81.6 + - - +
41H GLY 3.5 20.2 + - - +
43H PHE 3.2 14.4 - - - +
45H THR* 3.8 3.2 + - - -
62H TRP* 3.7 14.5 - - + -
67H PHE* 5.5 0.2 - - - -
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Residues in contact with GLN 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H GLN* 3.8 11.6 - - - +
27H HIS* 4.0 16.0 + - - -
39H ASN* 1.3 87.3 + - - +
41H GLY* 1.3 64.5 + - - +
42H SER 3.0 1.2 + - - -
43H PHE* 2.9 26.5 + - + +
45H THR* 3.5 18.8 - - + +
281K ALA 5.2 2.4 + - - -
283K THR* 3.6 23.6 + - - -
471K GLY* 6.1 0.2 - - - -
472K GLY* 3.4 37.2 - - - +
473K GLY* 3.5 11.2 - - - -
474K ASP* 3.7 18.4 + - - +
477K ASP* 4.4 4.3 - - - +
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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