Contacts of the strand formed by residues 46 - 52 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ARG* 4.0 17.9 - - - +
38D GLU* 4.2 9.9 - - + +
39D ILE 3.5 9.4 - - - +
40D GLU* 3.7 22.9 - - + +
44D GLY 3.3 17.0 + - - +
45D THR* 1.3 78.0 - - - +
47D GLY* 1.3 69.2 + - - +
48D ILE* 4.1 15.7 - - + +
116D LEU* 4.0 4.0 - - - -
119D LYS* 3.0 30.4 + - - +
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Residues in contact with GLY 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLU* 3.5 1.0 - - - -
39D ILE 2.8 37.6 + - - -
46D VAL* 1.3 71.4 - - - +
48D ILE* 1.3 66.3 + - - +
112D ALA* 3.5 23.4 - - - +
115D ASP* 3.2 8.1 - - - -
116D LEU* 3.7 13.5 - - - +
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Residues in contact with ILE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 4.6 5.4 - - + -
37D ILE 3.5 6.1 - - - +
38D GLU* 3.8 27.4 - - + -
46D VAL* 4.1 12.6 - - + +
47D GLY* 1.3 80.6 - - - +
49D GLY* 1.3 70.3 + - - +
112D ALA* 3.8 7.7 - - - -
115D ASP* 2.8 12.5 + - - +
119D LYS* 4.7 6.3 - - - +
305D ILE* 4.2 18.4 - - + -
356D LEU* 3.8 15.4 - - - +
358D PHE* 3.6 30.0 - - + -
360D LEU* 3.9 24.7 - - + -
362D GLU* 6.1 0.4 - - - +
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Residues in contact with GLY 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.5 3.8 - - - +
37D ILE* 2.9 38.0 + - - +
48D ILE* 1.3 78.6 - - - +
50D GLU* 1.3 62.9 + - - +
108D GLY 3.9 0.9 - - - -
111D MSE 3.8 26.9 - - - -
112D ALA* 3.8 1.2 - - - +
305D ILE* 3.9 4.7 - - - -
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D VAL* 3.7 14.0 - - + +
35D ASN 3.4 10.1 - - - +
36D LEU* 4.0 10.5 - - + +
37D ILE* 3.9 1.7 - - - +
49D GLY* 1.3 74.8 - - - +
51D CYS* 1.3 63.9 + - - +
107D SER* 4.5 3.3 + - - -
108D GLY* 3.3 15.5 + - - -
111D MSE 3.7 9.2 - - - +
302D THR* 3.2 8.1 - - + -
303D THR* 2.6 51.3 + - - +
305D ILE* 3.6 21.1 - - + +
306D THR* 2.6 33.7 + - - +
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Residues in contact with CYS 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D VAL* 3.4 9.1 - - - +
35D ASN* 3.0 37.4 + - + +
37D ILE* 5.0 0.2 - - - -
50D GLU* 1.3 72.3 - - - +
52D THR* 1.3 70.0 + - - +
53D VAL* 3.9 0.2 - - - +
64D LEU* 3.8 26.2 - - + -
104D GLN 3.6 12.1 - - - +
105D ILE* 3.1 36.6 - - + -
107D SER* 6.0 0.7 - - - -
108D GLY* 3.6 18.2 - - - -
302D THR* 5.2 2.7 - - - -
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Residues in contact with THR 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ALA 4.7 4.5 - - - -
35D ASN* 4.6 0.9 + - - -
51D CYS* 1.3 85.7 - - - +
53D VAL* 1.3 61.7 + - - +
54D ALA* 4.9 2.0 - - - -
60D THR* 4.3 4.2 + - - -
104D GLN* 3.1 40.5 + - - +
105D ILE* 5.2 0.7 - - - +
273D ARG* 3.6 39.3 + - + +
300D SER* 4.1 5.6 - - - -
301D PHE* 5.0 5.2 - - + +
302D THR* 3.7 26.0 - - + -
94E HIS 5.6 2.2 - - - +
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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