Contacts of the strand formed by residues 7 - 14 (chain A) in PDB entry 5ODS
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.2 36.9 - - + +
6A PRO* 1.3 86.6 - - + +
8A ARG* 1.3 60.7 + - - +
9A PHE* 3.7 30.1 - - + +
274A PHE* 5.3 0.2 - - + -
282A ILE* 5.6 0.9 - - + -
284A LEU* 3.8 33.7 - - + -
294A TYR* 3.6 38.4 - - + +
296A ASN* 5.8 0.9 - - - +
298A ILE* 5.2 6.3 - - + -
327A VAL* 3.9 20.0 - - + -
328A CYS 3.3 9.6 - - - +
329A VAL* 5.4 0.7 - - - -
330A GLU* 3.9 6.3 - - - +
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Residues in contact with ARG 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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5A LEU* 5.4 0.2 - - - -
7A ILE* 1.3 74.9 - - - +
9A PHE* 1.3 63.7 + - - +
10A GLN* 3.8 9.5 + - + +
312A THR* 4.1 16.4 - - - +
326A SER* 3.4 13.3 + - - +
328A CYS* 2.8 51.0 + - - +
329A VAL 4.1 10.5 + - - -
330A GLU* 3.0 39.5 + - + +
331A GLU* 4.5 9.3 + - - +
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Residues in contact with PHE 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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5A LEU* 5.5 2.3 - - + +
7A ILE* 3.7 21.3 + - + +
8A ARG* 1.3 76.1 - - - +
10A GLN* 1.3 72.9 + - - +
11A GLU* 5.1 3.6 - - + -
298A ILE* 3.6 44.2 - - + -
325A LEU* 3.6 42.8 - - + -
326A SER 3.3 3.4 - - - -
327A VAL* 3.5 20.0 - - + -
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Residues in contact with GLN 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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8A ARG* 4.6 11.4 - - + +
9A PHE* 1.3 86.1 - - - +
11A GLU* 1.3 81.4 + - - +
12A HIS* 3.4 31.3 + - + -
325A LEU* 3.4 4.5 - - - +
326A SER* 2.7 43.8 + - - +
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Residues in contact with GLU 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 PHE* 5.1 3.9 - - + -
10A GLN* 1.3 83.4 + - - +
12A HIS* 1.3 64.5 + - - +
13A LEU* 4.3 20.5 + - - +
14A GLN* 4.4 9.4 + - - +
323A GLN* 3.0 35.0 + - + +
324A VAL 3.8 4.3 - - - +
325A LEU* 3.9 19.5 - - + -
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Residues in contact with HIS 12 (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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10A GLN* 3.4 33.2 + - + +
11A GLU* 1.3 75.6 - - - +
13A LEU* 1.3 75.8 + - + +
55A MET* 4.7 7.6 - - + -
309A HIS* 3.2 27.8 + + - -
316A ILE* 4.1 14.1 - - + -
324A VAL* 2.9 23.8 + - + +
326A SER* 3.3 27.4 - - - -
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Residues in contact with LEU 13 (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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11A GLU* 3.5 10.8 - - - +
12A HIS* 1.3 88.3 - - + +
14A GLN* 1.3 59.2 + - - +
15A LEU* 3.8 29.6 - - + -
18A LEU* 3.8 20.6 - - + -
38A ILE* 5.1 0.4 - - + -
53A ILE* 5.1 2.9 - - + -
55A MET* 3.9 28.5 - - + -
58A PRO* 3.8 28.9 - - + -
322A GLY 3.6 1.2 - - - +
323A GLN* 3.7 2.1 - - - -
324A VAL* 2.8 43.7 + - + +
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Residues in contact with GLN 14 (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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11A GLU* 4.4 11.0 + - - +
13A LEU* 1.3 75.6 - - - +
15A LEU* 1.3 57.8 + - - +
16A GLN* 3.3 21.4 - - + +
17A ASN* 3.0 50.3 + - - +
18A LEU* 4.0 5.5 + - - +
321A LYS* 2.9 26.5 + - - +
322A GLY* 3.1 17.2 - - - +
323A GLN* 3.5 24.0 - - - +
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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