Contacts of the strand formed by residues 46 - 52 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.7 23.1 - - - +
38A GLU* 4.0 14.1 - - + +
39A ILE 3.4 11.2 - - - +
40A GLU* 3.6 18.8 - - + +
44A GLY 3.3 16.4 + - - +
45A THR* 1.3 76.7 - - - +
47A GLY* 1.3 73.8 + - - +
48A ILE* 4.2 10.1 - - + +
116A LEU* 4.3 2.9 - - - -
119A LYS* 2.9 30.2 + - - +
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.4 4.0 - - - -
39A ILE* 2.8 37.0 + - - -
46A VAL* 1.3 74.2 - - - +
48A ILE* 1.3 60.9 + - - +
112A ALA* 3.4 25.2 - - - +
115A ASP* 3.2 8.3 - - - -
116A LEU* 3.8 12.2 - - - +
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Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 5.2 4.3 - - + -
37A ILE 3.5 5.6 - - - +
38A GLU* 3.9 23.3 - - + -
46A VAL* 4.2 12.3 - - + +
47A GLY* 1.3 81.1 - - - +
49A GLY* 1.3 71.4 + - - +
112A ALA* 3.7 10.8 - - - +
115A ASP* 2.8 12.5 + - - +
119A LYS* 4.4 9.6 - - - +
305A ILE* 4.1 12.6 - - + -
356A LEU* 3.8 12.1 - - - +
358A PHE* 3.7 28.9 - - + -
360A LEU* 3.7 35.0 - - + -
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.5 3.8 - - - +
37A ILE* 2.9 32.1 + - - +
48A ILE* 1.3 79.8 - - - +
50A GLU* 1.3 64.3 + - - +
108A GLY 3.7 15.9 - - - -
111A MSE 3.8 10.3 - - - -
112A ALA* 3.6 1.4 - - - +
305A ILE* 4.1 10.3 - - - -
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.5 12.4 - - + +
35A ASN 3.4 9.6 - - - +
36A LEU* 3.7 17.1 - - + +
37A ILE* 3.8 3.1 - - - +
49A GLY* 1.3 76.0 - - - +
51A CYS* 1.3 64.4 + - - +
107A SER* 4.6 3.1 + - - -
108A GLY* 3.4 14.3 + - - -
111A MSE 3.8 11.6 - - - +
302A THR* 4.0 9.1 - - + +
303A THR* 2.8 47.9 + - - +
305A ILE* 3.7 9.4 - - + -
306A THR* 2.7 41.7 + - - +
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Residues in contact with CYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.4 9.8 - - - +
35A ASN* 3.0 35.4 + - + +
37A ILE* 5.1 0.2 - - - -
50A GLU* 1.3 75.1 - - - +
52A THR* 1.3 70.1 + - - +
64A LEU* 3.9 25.8 - - + -
104A GLN 3.7 13.7 - - - +
105A ILE* 3.2 34.5 - - + -
107A SER* 6.0 0.4 - - - -
108A GLY* 3.6 18.4 - - - -
302A THR* 5.1 1.3 - - - -
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Residues in contact with THR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA 4.6 5.2 - - - +
35A ASN* 4.8 0.7 + - - -
51A CYS* 1.3 85.6 - - - +
53A VAL* 1.3 62.2 + - - +
54A ALA* 4.9 2.2 - - - -
60A THR* 4.4 4.5 + - - -
104A GLN* 3.2 39.1 + - - +
273A ARG* 3.6 36.9 + - + +
300A SER* 4.0 8.1 - - - +
301A PHE* 5.0 6.1 - - + +
302A THR* 3.7 26.2 - - + -
94G HIS 5.7 1.6 - - - +
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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