Contacts of the strand formed by residues 6 - 11 (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 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A TYR* 1.3 81.3 + - - +
7A ILE* 1.3 66.8 + - - +
20A VAL* 3.5 4.2 - - - -
21A ILE* 2.9 50.8 + - - +
22A THR 5.4 2.1 + - - -
756A PRO* 4.8 0.2 - - - -
757A GLU* 4.4 2.8 - - - +
758A ASN* 3.5 35.8 + - - -
760A VAL* 6.0 2.5 - - - -
991A ALA* 6.0 0.7 - - - -
995A THR* 4.8 8.3 + - - -
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Residues in contact with ILE 7 (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* 4.0 24.9 - - + -
6A SER* 1.3 78.8 - - - +
8A GLY* 1.3 66.8 + - - +
9A LEU* 4.2 19.7 - - + -
19A ALA 3.4 9.2 - - - +
20A VAL* 4.3 7.6 - - + -
744A VAL* 5.1 9.0 - - + +
747A LEU* 4.4 34.1 - - + -
748A VAL* 4.9 9.4 - - + -
756A PRO* 4.3 15.9 - - + -
758A ASN 2.9 8.9 + - - +
759A ILE* 3.3 17.1 - - + +
760A VAL* 2.9 26.2 + - - +
991A ALA* 4.6 2.9 - - - -
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Residues in contact with GLY 8 (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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7A ILE* 1.3 74.9 - - - +
9A LEU* 1.3 63.4 + - - +
17A GLY 3.9 0.2 - - - +
18A TRP* 3.5 4.9 - - - -
19A ALA 2.9 34.0 + - - +
760A VAL* 3.7 6.1 - - - -
987A ALA* 3.9 9.5 - - - +
991A ALA* 3.7 27.6 - - - +
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Residues in contact with LEU 9 (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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7A ILE* 4.2 9.2 - - + -
8A GLY* 1.3 74.6 - - - +
10A ASP* 1.3 61.3 + - - +
11A ILE* 4.2 3.1 - - + -
16A VAL* 4.6 4.5 - - + -
17A GLY 3.3 6.1 - - - +
18A TRP* 3.7 27.4 - - + -
740A THR* 3.8 22.9 - - + -
743A VAL* 4.4 12.3 - - + -
744A VAL* 3.7 27.4 - - + -
747A LEU* 5.9 0.7 - - + -
759A ILE* 4.3 9.4 - - + -
760A VAL* 2.9 12.5 + - - +
761A ILE* 3.7 24.6 - - + -
762A GLU* 3.0 27.4 + - - +
935A LEU* 4.8 0.7 - - + -
987A ALA* 4.5 3.7 + - - +
990A ASN* 4.4 4.8 - - - +
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Residues in contact with ASP 10 (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* 1.3 74.0 - - - +
11A ILE* 1.3 82.0 + - - +
12A GLY* 5.2 0.2 - - - -
15A SER* 4.3 0.8 - - - +
16A VAL* 3.5 5.7 - - - +
17A GLY 2.9 34.7 + - - +
762A GLU* 3.7 11.6 - - - +
764A ALA* 3.8 16.3 + - - +
983A HIS* 4.3 14.8 + - - +
986A ASP* 3.4 26.4 - - - +
987A ALA* 4.0 18.1 - - + +
990A ASN* 4.3 8.3 - - - +
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Residues in contact with ILE 11 (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* 4.9 4.3 - - + -
10A ASP* 1.3 85.9 + - - +
12A GLY* 1.3 71.0 + - - +
15A SER 4.2 1.6 - - - -
16A VAL* 4.8 4.7 - - + -
733A ILE* 5.3 4.3 - - + -
736A GLY* 4.6 12.6 - - - +
737A ILE* 5.0 3.6 - - + +
740A THR* 3.5 42.0 - - + +
761A ILE* 4.3 21.5 - - + -
762A GLU 2.9 12.8 + - - +
763A MET* 3.8 31.2 - - + +
764A ALA* 3.2 25.6 + - - +
931A VAL* 4.8 10.8 - - + -
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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