Contacts of the strand formed by residues 15 - 21 (chain A) in PDB entry 6O0Z
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 SER 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASP* 4.3 0.5 - - - +
12A GLY* 2.9 33.3 + - - +
13A THR 3.7 1.0 - - - -
14A ASN* 1.3 83.8 - - - +
16A VAL* 1.3 66.3 + - - +
17A GLY 5.1 0.3 + - - -
51A LEU 3.2 7.0 - - - -
52A LEU* 3.7 9.6 - - - -
53A PHE* 3.9 3.5 - - - -
983A HIS* 3.2 49.7 + - - +
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Residues in contact with VAL 16 (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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9A LEU* 4.6 7.4 - - + -
10A ASP 3.5 10.3 - - - +
11A ILE* 4.8 5.8 - - + -
15A SER* 1.3 79.2 - - - +
17A GLY* 1.3 65.4 + - - +
18A TRP* 4.1 4.8 - - + +
50A ALA* 3.3 3.9 - - - -
51A LEU* 2.9 42.5 + - + +
53A PHE* 4.1 18.4 - - + -
736A GLY* 3.9 23.8 - - - +
739A GLN* 4.6 5.4 - - + +
740A THR* 4.0 13.2 - - + +
743A VAL* 4.4 21.8 - - + -
983A HIS* 5.3 0.2 - - - -
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Residues in contact with GLY 17 (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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9A LEU* 3.3 7.4 - - - +
10A ASP* 2.9 36.8 + - - +
15A SER* 4.3 1.0 + - - -
16A VAL* 1.3 74.2 - - - +
18A TRP* 1.3 60.3 + - - +
49A GLY 3.6 8.1 - - - -
50A ALA* 4.1 3.8 - - - -
983A HIS* 4.1 22.9 - - - +
987A ALA* 3.4 7.5 - - - +
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Residues in contact with TRP 18 (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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8A GLY 3.5 5.6 - - - +
9A LEU* 3.7 17.7 - - + -
16A VAL* 4.1 11.0 - - + -
17A GLY* 1.3 76.9 - - - +
19A ALA* 1.3 66.4 + - - +
20A VAL* 4.7 1.1 - - + -
47A LEU* 3.5 10.1 - - + -
48A ILE* 3.5 31.4 - - - +
49A GLY* 2.9 54.4 + - - +
50A ALA 3.7 9.6 + - - +
51A LEU* 5.2 3.6 - - + +
743A VAL* 4.0 22.5 - - + +
747A LEU* 3.6 37.7 - - + -
984A ALA* 4.8 0.2 - - - +
987A ALA* 3.8 2.4 - - - +
1093A ASN* 4.0 11.9 - - + -
1352A ILE 5.5 0.6 + - - -
1353A THR* 3.7 33.5 - - - +
1355A LEU* 4.3 15.3 - - + -
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Residues in contact with ALA 19 (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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6A SER 4.0 0.2 - - - +
7A ILE* 3.4 7.3 - - - +
8A GLY* 2.9 32.4 + - - +
18A TRP* 1.3 77.9 - - - +
20A VAL* 1.3 64.5 + - - +
21A ILE* 4.2 2.6 + - + -
27A VAL* 6.1 0.9 - - + -
47A LEU 4.1 5.6 - - - -
48A ILE* 4.1 13.2 - - + +
987A ALA* 4.2 3.1 - - + +
988A TYR* 3.8 42.2 - - + +
991A ALA* 5.1 1.0 - - + +
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Residues in contact with VAL 20 (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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5A TYR* 4.1 23.3 - - + -
6A SER 3.5 2.7 - - - -
7A ILE* 4.3 10.3 - - + -
18A TRP* 4.7 0.7 - - + -
19A ALA* 1.3 77.7 - - - +
21A ILE* 1.3 65.3 + - - +
27A VAL* 3.5 12.5 - - - +
28A PRO* 3.3 27.3 - - + +
47A LEU* 3.3 22.8 + - + +
747A LEU* 3.8 37.0 - - + -
751A MET* 4.5 21.8 - - + -
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Residues in contact with ILE 21 (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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5A TYR* 3.3 6.9 - - - +
6A SER* 2.9 53.6 + - - +
19A ALA* 5.0 1.6 - - + -
20A VAL* 1.3 81.1 - - - +
22A THR* 1.3 72.5 + - - +
25A TYR* 4.6 11.4 - - + -
26A LYS 4.2 4.5 - - - +
27A VAL* 5.0 4.7 - - + +
988A TYR* 3.7 36.1 - - + -
991A ALA* 3.8 37.7 - - + -
992A VAL* 4.1 5.4 - - + +
995A THR* 4.0 17.7 - - + -
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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