Contacts of the strand formed by residues 18 - 25 (chain N) in PDB entry 4R2G
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 LEU 18 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9N PRO* 4.2 5.8 - - + -
12N VAL* 3.8 14.4 - - + +
16N GLU 3.9 2.2 + - - -
17N THR* 1.3 79.3 - - - +
19N SER* 1.3 78.2 + - - +
20N VAL* 3.6 31.4 - - + +
80N LEU 5.4 0.2 - - - +
81N GLN* 3.2 3.4 - - - -
82N LEU* 2.9 60.7 + - + +
86N ASP 4.4 2.9 - - - +
90N TYR* 3.4 43.3 - - + +
109N VAL* 3.7 26.9 - - + -
111N VAL* 5.9 0.2 - - + -
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Residues in contact with SER 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N SER 4.7 0.2 - - - +
8N GLY* 4.6 0.9 - - - -
9N PRO* 3.3 22.9 - - - +
17N THR 3.6 1.4 + - - -
18N LEU* 1.3 80.9 - - - +
20N VAL* 1.3 61.0 + - - +
21N THR* 5.1 2.9 + - - -
80N LEU 3.4 6.1 - - - -
81N GLN* 3.3 28.7 + - - -
200O VAL* 3.9 17.1 - - - +
202O THR* 4.7 13.9 - - - -
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Residues in contact with VAL 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N SER 3.5 13.7 - - - +
8N GLY* 3.8 6.5 - - - -
18N LEU* 3.6 22.2 - - + +
19N SER* 1.3 76.3 + - - +
21N THR* 1.3 66.9 + - - +
36N TRP* 3.8 24.9 - - + -
79N SER* 3.6 1.7 - - - -
80N LEU* 2.9 51.2 + - + +
90N TYR* 4.2 12.6 - - + -
107N THR* 3.9 10.3 - - + -
109N VAL* 3.7 18.6 - - + -
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Residues in contact with THR 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N GLU* 3.1 6.2 - - - +
7N SER* 2.8 55.6 + - - +
19N SER* 5.1 3.3 + - - -
20N VAL* 1.3 78.2 + - - +
22N CYS* 1.3 66.9 + - - +
23N ILE* 4.1 8.5 - - + -
36N TRP* 3.7 4.9 - - - -
77N GLN* 2.7 38.5 + - + +
78N LEU 3.8 2.9 - - - -
79N SER* 3.9 8.1 - - - -
81N GLN* 5.6 0.2 + - - -
200O VAL* 5.9 2.3 - - - +
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Residues in contact with CYS 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N LEU* 3.6 26.7 - - - -
5N GLN 3.5 9.4 - - - -
6N GLU* 4.5 0.4 - - + -
21N THR* 1.3 74.6 - - - +
23N ILE* 1.3 63.3 + - - +
24N VAL* 3.9 8.5 + - - +
36N TRP* 3.9 5.5 - - + -
77N GLN* 3.7 4.2 - - - +
78N LEU* 2.9 42.8 + - + +
92N CYS* 2.0 48.9 - - + -
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Residues in contact with ILE 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N LEU* 4.1 0.3 - - - -
5N GLN* 2.9 37.4 + - + +
7N SER* 5.0 4.0 - - - +
21N THR* 4.1 11.0 - - + -
22N CYS* 1.3 73.5 - - - +
24N VAL* 1.3 70.4 + - - +
25N SER* 3.8 8.4 + - - +
75N LYS* 4.4 13.9 - - + +
76N ASN 4.1 2.7 - - - +
77N GLN* 3.9 35.0 - - + +
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Residues in contact with VAL 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2N VAL* 4.0 7.4 - - + -
3N GLN 3.7 3.4 - - - +
4N LEU* 4.5 8.1 - - + -
22N CYS* 4.5 9.2 - - - +
23N ILE* 1.3 80.4 - - - +
25N SER* 1.3 72.0 + - - +
27N GLY 4.0 11.2 - - - +
29N ILE* 3.4 28.5 - - + +
34N TRP* 3.6 37.2 - - + -
76N ASN* 2.4 41.9 + - - +
78N LEU* 5.2 0.9 - - + -
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Residues in contact with SER 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1N GLN 4.6 0.2 - - - -
2N VAL* 3.3 7.3 - - - +
3N GLN* 2.9 47.4 + - - +
4N LEU* 5.1 0.7 - - - -
5N GLN* 5.9 1.0 - - - +
23N ILE* 3.8 8.5 + - - +
24N VAL* 1.3 75.3 - - - +
26N GLY* 1.3 63.7 + - - +
27N GLY 3.2 4.5 + - - -
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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