Contacts of the strand formed by residues 47 - 52 (chain G) in PDB entry 3SZ9
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 VAL 47 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38G PRO* 3.8 34.3 - - + -
39G THR 3.7 4.7 - - - +
40G VAL* 4.3 9.0 - - + +
45G GLY 5.5 0.9 - - - +
46G GLU* 1.3 76.4 - - - +
48G ILE* 1.3 64.7 + - - +
49G CYS* 3.7 21.1 - - - +
50G GLN* 4.5 6.7 - - + +
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Residues in contact with ILE 48 (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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17G VAL* 4.1 15.7 - - + +
39G THR* 2.7 14.5 + - + +
40G VAL 3.6 1.6 - - - -
41G ASN* 3.5 28.9 - - + +
46G GLU 3.4 0.4 + - - -
47G VAL* 1.3 74.9 - - - +
49G CYS* 1.3 62.2 + - - +
108G LEU* 3.5 45.5 - - + +
109G ASP* 3.6 27.8 - - + +
199G LEU* 3.8 20.9 - - + -
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Residues in contact with CYS 49 (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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17G VAL* 4.1 18.6 - - + -
20G ASN* 4.5 5.6 - - - +
38G PRO* 3.5 1.9 - - - +
39G THR* 3.0 27.3 + - - +
47G VAL* 3.7 11.1 - - - +
48G ILE* 1.3 86.2 - - + +
50G GLN* 1.3 71.9 + - - +
51G VAL* 4.3 0.2 - - - -
199G LEU* 3.9 36.3 - - - -
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Residues in contact with GLN 50 (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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20G ASN* 3.0 31.6 + - - +
36G THR* 2.5 43.6 + - + +
37G PHE* 3.4 13.1 - - - -
38G PRO* 3.6 28.9 - - - +
47G VAL* 4.5 7.4 - - + +
49G CYS* 1.3 76.8 - - - +
51G VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 51 (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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20G ASN* 3.3 17.0 - - + +
36G THR* 3.2 4.8 - - - -
37G PHE* 2.8 59.0 + - + +
39G THR* 4.1 11.9 - - + -
49G CYS* 4.3 0.4 - - - +
50G GLN* 1.3 80.9 - - - +
52G ALA* 1.3 66.4 + - - +
198G PRO* 4.0 12.6 - - + -
199G LEU* 3.9 26.0 - - + -
202G LEU* 4.2 7.2 - - + -
222G PRO* 3.7 22.0 - - + -
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Residues in contact with ALA 52 (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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20G ASN 2.9 15.7 + - - +
21G GLN* 3.9 17.5 - - + -
22G ILE* 3.9 12.6 - - + +
29G HIS 4.3 1.6 - - - +
30G ASP* 4.6 3.8 - - - +
31G ALA 3.9 22.0 - - - +
35G LYS 3.8 6.1 - - - -
36G THR* 4.4 6.0 - - + +
37G PHE* 3.5 5.1 - - - -
51G VAL* 1.3 71.9 - - - +
53G GLU* 1.3 60.2 + - - +
54G GLY 3.3 6.3 + - - -
222G PRO* 3.5 17.7 - - - +
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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