Contacts of the strand formed by residues 46 - 52 (chain G) in PDB entry 2PGW
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 46 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G ARG* 4.1 11.4 - - - +
38G GLU* 4.0 22.7 - - + -
39G ILE 3.3 9.0 - - - +
40G GLU* 3.8 18.8 - - + +
44G GLY 3.4 15.9 + - - +
45G THR* 1.3 77.6 - - - +
47G GLY* 1.3 70.9 + - - +
48G ILE* 4.3 10.7 - - + +
116G LEU* 4.5 1.8 - - - -
119G LYS* 3.0 30.2 + - - +
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Residues in contact with GLY 47 (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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38G GLU* 3.3 4.2 - - - -
39G ILE* 2.8 36.6 + - - -
46G VAL* 1.3 74.5 - - - +
48G ILE* 1.3 61.2 + - - +
112G ALA* 3.5 23.8 - - - +
115G ASP* 3.2 9.6 - - - -
116G LEU* 3.8 12.8 - - - +
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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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36G LEU* 5.1 4.3 - - + -
37G ILE 3.5 6.1 - - - +
38G GLU* 4.2 20.2 - - + +
46G VAL* 4.3 16.8 - - + +
47G GLY* 1.3 80.4 - - - +
49G GLY* 1.3 72.3 + - - +
112G ALA* 3.7 10.5 - - - +
115G ASP* 2.8 11.2 + - - +
119G LYS* 4.5 9.2 - - - +
305G ILE* 4.1 20.0 - - + -
356G LEU* 3.8 13.0 - - - +
358G PHE* 3.7 28.0 - - + -
360G LEU* 3.6 29.2 - - + -
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Residues in contact with GLY 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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36G LEU* 3.5 4.0 - - - +
37G ILE* 2.9 30.7 + - - -
48G ILE* 1.3 80.8 - - - +
50G GLU* 1.3 64.4 + - - +
108G GLY 3.7 16.8 - - - -
111G MSE 3.9 13.9 - - - -
112G ALA* 3.7 1.0 - - - +
305G ILE* 4.0 5.4 - - - -
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Residues in contact with GLU 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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34G VAL* 3.6 15.4 - - + +
35G ASN 3.3 9.4 - - - +
36G LEU* 3.7 17.4 - - + +
37G ILE* 3.8 3.1 - - - +
49G GLY* 1.3 75.4 - - - +
51G CYS* 1.3 64.1 + - - +
107G SER* 4.7 2.8 + - - -
108G GLY* 3.4 14.6 + - - -
111G MSE 3.8 9.0 - - - +
302G THR* 3.2 7.1 - - + +
303G THR* 2.7 50.9 + - - +
305G ILE* 3.7 12.3 - - + -
306G THR* 2.7 33.8 + - - +
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Residues in contact with CYS 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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34G VAL* 3.4 9.2 - - - +
35G ASN* 2.9 35.7 + - + +
50G GLU* 1.3 74.0 - - - +
52G THR* 1.3 70.9 + - - +
64G LEU* 3.8 26.7 - - + -
104G GLN 3.6 16.4 - - - +
105G ILE* 3.2 35.9 - - + -
107G SER* 6.1 0.4 - - - -
108G GLY* 3.7 15.0 - - - -
302G THR* 5.2 2.0 - - - -
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Residues in contact with THR 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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94A HIS 5.7 1.6 - - - -
33G ALA 4.6 4.7 - - - -
35G ASN* 4.7 0.9 + - - -
51G CYS* 1.3 84.9 - - - +
53G VAL* 1.3 62.0 + - - +
54G ALA* 5.0 2.2 - - - -
60G THR* 4.4 3.8 + - - -
104G GLN* 3.3 36.6 + - - +
105G ILE* 5.3 0.9 - - - +
273G ARG* 3.6 29.4 + - + +
300G SER* 4.0 17.3 - - - +
301G PHE* 4.7 7.2 - - + +
302G THR* 3.5 28.2 - - + +
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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