Contacts of the strand formed by residues 40 - 47 (chain A) in PDB entry 4GNR
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 THR 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LYS* 1.3 94.0 + - - +
41A ILE* 1.3 65.0 + - - +
42A LYS* 4.1 8.3 + - - +
80A LYS* 4.3 2.7 - - - -
81A GLN* 3.2 25.1 - - + +
83A GLU* 2.8 37.2 + - + +
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Residues in contact with ILE 41 (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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39A LYS* 5.7 0.9 - - - +
40A THR* 1.3 75.7 - - - +
42A LYS* 1.3 58.5 + - - +
43A ILE* 3.8 23.4 + - + -
77A ILE* 3.8 43.3 - - + +
78A ASP* 5.6 1.1 - - + +
80A LYS* 3.9 24.5 - - + +
81A GLN 2.9 7.4 + - - +
82A ILE* 3.3 13.2 - - + +
83A GLU 2.7 29.7 + - - +
110A SER* 4.8 9.6 - - - +
330A ALA* 4.4 20.9 - - + +
339A ILE* 5.4 2.5 - - + -
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Residues in contact with LYS 42 (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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40A THR* 4.0 6.2 + - - +
41A ILE* 1.3 73.6 - - - +
43A ILE* 1.3 67.2 + - - +
83A GLU* 3.3 42.8 + - - +
85A VAL* 4.1 18.1 - - - +
106A GLN 5.3 0.2 + - - -
107A SER* 2.8 33.7 + - - +
108A LYS 4.5 4.7 - - - +
109A VAL* 4.0 15.7 - - + -
110A SER* 2.9 33.1 + - - +
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Residues in contact with ILE 43 (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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41A ILE* 4.1 18.2 - - + -
42A LYS* 1.3 85.5 - - - +
44A GLY* 1.3 71.8 + - - +
45A PHE* 4.4 9.2 - - + -
68A VAL* 5.9 1.8 - - + -
82A ILE* 3.8 29.4 - - + -
83A GLU 2.9 8.5 + - - -
84A VAL* 3.3 8.8 - - + +
85A VAL 3.0 22.4 + - - -
109A VAL* 4.1 2.2 - - - -
110A SER* 4.8 1.6 - - - -
111A ALA* 3.6 29.6 - - + +
113A VAL* 4.1 19.7 - - + -
323A VAL* 6.0 2.7 - - + -
326A VAL* 4.0 15.9 - - + -
330A ALA* 6.1 0.4 - - + -
339A ILE* 5.5 1.6 - - + -
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Residues in contact with GLY 44 (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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43A ILE* 1.3 76.2 - - - +
45A PHE* 1.3 66.9 + - - -
85A VAL 3.3 9.2 - - - -
103A LEU* 4.0 11.9 - - - -
109A VAL* 3.7 17.6 - - - +
111A ALA 2.9 13.1 + - - -
112A VAL* 3.3 3.6 - - - -
113A VAL 2.9 25.5 + - - -
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Residues in contact with PHE 45 (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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43A ILE* 4.4 12.3 - - + -
44A GLY* 1.3 81.7 - - - -
46A ASN* 1.3 59.8 + - - +
47A PHE* 3.6 29.2 - + + -
61A GLN* 4.2 6.3 - - + -
64A ALA* 3.6 35.4 - - + -
65A GLN* 3.7 23.8 - - - -
68A VAL* 4.1 9.0 - - + -
84A VAL* 3.7 30.3 - - + -
85A VAL 2.9 7.8 + - - +
86A ASP* 3.7 29.8 - - - +
87A LYS* 2.9 29.5 + - - +
103A LEU* 3.8 3.5 - - - +
113A VAL* 3.3 9.4 - - + -
323A VAL* 4.5 5.6 - - + -
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Residues in contact with ASN 46 (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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45A PHE* 1.3 73.9 - - - +
47A PHE* 1.3 59.0 + - - +
87A LYS 3.6 3.1 - - - -
89A ASN* 2.9 28.9 + - - +
96A ALA* 3.1 14.0 + - - -
99A VAL* 3.6 18.8 - - + +
100A THR* 2.9 29.3 + - - +
103A LEU* 4.2 1.3 - - + -
112A VAL* 4.0 18.1 - - + +
113A VAL 2.9 8.3 + - - -
114A GLY* 3.3 6.9 + - - +
115A PRO* 3.0 39.8 - - - +
124A ALA* 4.3 0.2 - - - +
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Residues in contact with PHE 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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45A PHE* 3.6 36.3 - + + -
46A ASN* 1.3 80.7 + - - +
48A GLU* 1.3 61.3 + - - +
49A GLU* 2.9 22.0 + - + +
57A GLY* 3.7 13.2 - - - +
60A GLU* 3.5 43.5 - - + -
61A GLN* 3.7 27.4 - - - -
64A ALA* 4.1 4.0 - - + -
87A LYS 3.1 7.7 + - - -
88A ASP* 3.3 6.1 - - - -
89A ASN* 2.9 27.0 + - - +
113A VAL* 3.8 25.6 - - + -
114A GLY* 3.5 19.1 - - - -
116A ALA 4.5 4.7 - - - -
138A PRO* 4.7 0.4 - - + -
319A ALA* 4.7 1.3 - - + -
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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