Contacts of the strand formed by residues 7 - 15 (chain N) in PDB entry 6CET
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 ILE 7 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N CYS* 4.1 2.9 - - - +
6N ARG* 1.3 92.8 + - - +
8N GLU* 1.3 70.0 + - - +
9N CYS 4.9 1.6 - - - +
10N ILE* 4.7 1.8 - - + -
87N PHE* 3.7 37.0 - - + -
88N VAL 5.0 0.4 - - - +
89N CYS* 3.6 23.6 - - - -
98N LEU* 3.9 14.4 - - + -
136N LEU* 3.8 25.8 - - + +
139N LEU* 4.1 23.3 - - + -
140N ASN* 3.5 28.7 + - - +
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Residues in contact with GLU 8 (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 ARG* 4.1 5.9 - - + +
7N ILE* 1.3 81.1 - - - +
9N CYS* 1.3 81.6 + - - +
28N PRO 3.6 14.7 - - - -
36N LEU* 4.2 18.8 - - + +
65N ILE* 4.6 9.7 - - - +
88N VAL* 3.6 6.3 + - + +
89N CYS* 3.2 36.5 + - - +
90N ASP* 3.5 12.8 + - - +
136N LEU* 3.7 14.2 - - - +
140N ASN* 5.8 0.4 - - - +
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Residues in contact with CYS 9 (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 ILE* 4.9 1.8 - - - +
8N GLU* 1.3 86.9 - - - +
10N ILE* 1.3 69.1 + - - +
11N PHE* 5.7 0.4 - - + -
26N GLN* 5.4 3.6 - - + +
27N VAL 3.5 8.1 - - - +
28N PRO* 3.7 10.8 - - - -
36N LEU* 3.2 55.0 - - + -
38N ASP* 5.8 2.9 - - - +
87N PHE* 3.8 2.1 - - - -
88N VAL* 2.9 48.8 + - + +
136N LEU* 4.4 1.5 - - - +
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Residues in contact with ILE 10 (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 ILE* 4.7 1.3 - - + -
9N CYS* 1.3 79.9 - - - +
11N PHE* 1.3 70.5 + - - +
26N GLN* 4.0 1.0 - - - +
27N VAL* 3.0 42.3 + - + +
85N LEU* 4.6 12.1 - - + -
86N GLY 3.7 12.1 - - - +
87N PHE* 3.7 30.3 - - + -
105N LEU* 6.6 0.4 - - + -
132N MET* 4.3 20.6 - - + +
135N LEU* 4.6 9.2 - - + -
136N LEU* 3.8 43.5 - - + +
139N LEU* 6.2 0.7 - - + -
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Residues in contact with PHE 11 (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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9N CYS* 5.7 0.4 - - + -
10N ILE* 1.3 81.8 - - - +
12N PHE* 1.3 69.1 + - - +
13N SER* 4.8 10.1 - - - -
24N THR* 5.4 6.5 - - + -
25N TYR 3.3 13.5 - - - +
26N GLN* 4.5 4.9 - - + -
27N VAL* 5.4 0.4 - - - -
38N ASP* 4.0 19.7 - - - +
43N TYR* 5.8 4.3 - + - -
50N LEU* 5.2 13.5 - - + -
68N PRO* 4.9 10.8 - - + -
69N VAL 4.8 2.5 - - - -
70N CYS* 5.9 3.1 - - + -
84N ASN* 5.8 2.5 - - - -
85N LEU* 3.4 9.6 - - - +
86N GLY* 2.9 65.8 + - - +
87N PHE 3.5 4.0 - - - -
88N VAL* 3.9 28.0 - - + -
132N MET* 6.0 3.4 - - - -
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Residues in contact with PHE 12 (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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11N PHE* 1.3 77.3 - - - +
13N SER* 1.3 73.5 + - - +
14N GLU* 4.4 15.0 - - + -
23N ILE* 5.6 3.1 - - + -
24N THR* 3.1 7.8 - - - +
25N TYR* 2.9 59.4 + + + +
83N PHE* 3.4 43.7 - + + -
84N ASN 3.7 11.0 - - - -
85N LEU* 4.5 13.5 - - + -
109N LEU* 5.2 8.1 - - + -
119N VAL* 5.7 7.2 - - + -
125N LYS* 5.1 17.0 - - + -
128N LEU* 5.0 15.0 - - + -
132N MET* 5.0 10.9 - - + +
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Residues in contact with SER 13 (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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11N PHE* 4.8 7.4 - - - -
12N PHE* 1.3 82.7 - - - +
14N GLU* 1.3 70.0 + - - +
23N ILE 2.8 9.4 + - - -
24N THR* 3.7 8.5 - - - -
43N TYR* 2.5 30.0 + - - -
50N LEU* 4.2 17.8 - - - +
83N PHE* 3.3 5.2 - - - +
84N ASN* 2.9 41.5 + - - +
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Residues in contact with GLU 14 (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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12N PHE* 4.4 10.1 - - + -
13N SER* 1.3 83.4 + - - +
15N PHE* 1.3 70.6 + - - +
16N HIS* 3.3 29.6 + - - +
17N PRO* 5.1 1.6 - - - +
22N LYS* 3.4 4.8 - - - +
23N ILE* 2.9 50.5 + - + +
43N TYR* 5.3 0.2 - - - -
81N LEU* 4.9 15.6 - - - +
82N LEU 3.5 16.9 + - - +
83N PHE* 3.8 15.3 - - + +
84N ASN* 5.4 0.2 - - - -
125N LYS* 4.2 18.5 - - - -
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Residues in contact with PHE 15 (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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14N GLU* 1.3 71.9 - - - +
16N HIS* 1.3 67.0 + - - +
17N PRO* 4.4 3.1 - - + +
21N PRO* 3.3 24.5 - - + -
22N LYS* 3.5 31.9 - - + +
50N LEU 5.3 7.3 + - - +
51N GLN* 5.5 7.6 - - + -
80N ALA 4.6 2.8 - - - +
81N LEU* 5.5 0.3 - - - -
82N LEU* 3.1 59.6 + - + +
83N PHE* 4.7 0.2 - - - +
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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