Contacts of the strand formed by residues 3 - 11 (chain A) in PDB entry 2POD
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 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS* 1.3 70.5 - - - +
4A THR* 1.3 62.2 + - - +
5A GLU 4.2 3.4 - - - +
6A ILE* 3.7 26.5 - - + -
22A VAL* 3.8 19.5 - - + -
23A HIS 3.5 10.3 - - - +
24A THR* 4.1 2.9 - - + -
53A LEU* 3.3 43.7 - - + +
54A ILE* 3.7 6.4 - - - +
55A GLY* 2.8 27.5 + - - -
56A GLU* 2.9 19.3 + - + +
57A ASP 4.8 0.4 - - - -
58A PRO* 3.9 35.0 - - + -
64A HIS* 5.1 1.3 - - - +
91A LEU* 4.0 6.3 - - + -
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Residues in contact with THR 4 (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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2A LYS* 3.9 4.5 - - + +
3A ILE* 1.3 75.2 - - - +
5A GLU* 1.3 69.8 + - - +
23A HIS* 2.9 24.0 + - - +
24A THR 3.6 4.9 + - - -
25A ASP* 3.5 32.1 - - + +
54A ILE* 3.9 19.1 - - - +
397A THR 4.2 2.8 - - - +
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Residues in contact with GLU 5 (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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3A ILE* 3.9 1.0 - - - +
4A THR* 1.3 86.2 + - - +
6A ILE* 1.3 63.6 + - - +
7A GLU* 3.9 4.3 - - - +
22A VAL* 3.6 1.7 - - - +
23A HIS* 2.7 60.8 + - + +
54A ILE* 4.8 0.7 - - - -
396A ASN* 2.9 41.0 + - - +
397A THR 3.6 8.3 - - - +
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Residues in contact with ILE 6 (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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3A ILE* 3.7 26.2 - - + -
5A GLU* 1.3 73.7 - - - +
7A GLU* 1.3 66.5 + - - +
8A THR* 4.8 3.6 - - + -
20A VAL* 3.9 20.9 - - + -
21A LEU 3.3 2.2 - - - -
22A VAL* 4.1 20.0 - - + -
45A ILE* 5.4 4.9 - - + -
46A HIS* 4.0 7.0 + - + +
50A ALA* 4.4 8.1 - - + +
53A LEU* 3.8 27.1 - - + -
54A ILE* 3.8 15.0 - - + -
87A LEU* 4.6 7.2 - - + -
395A ARG 3.9 0.7 - - - +
396A ASN* 3.7 3.3 + - - -
397A THR* 3.2 47.2 + - + +
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Residues in contact with GLU 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 GLU* 3.9 5.3 - - - +
6A ILE* 1.3 76.1 - - - +
8A THR* 1.3 62.1 + - - +
9A LEU* 4.6 6.7 - - + +
20A VAL* 3.4 5.0 - - - +
21A LEU* 2.7 58.7 + - + +
23A HIS* 2.8 28.5 + - - +
387A ARG* 3.4 27.4 + - - -
394A VAL* 4.7 9.2 - - + +
395A ARG 3.3 6.3 - - - +
396A ASN* 3.3 27.3 - - - +
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Residues in contact with THR 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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6A ILE* 4.8 2.5 - - + -
7A GLU* 1.3 77.5 - - - +
9A LEU* 1.3 66.0 + - - +
18A LEU* 4.0 6.3 - - + -
19A TRP 3.4 8.7 - - - +
20A VAL* 4.4 7.0 - - + -
42A GLU* 2.7 30.3 + - + -
45A ILE* 3.8 30.5 - - + -
46A HIS* 2.8 32.8 + - + +
393A ALA 3.8 0.7 - - - +
394A VAL* 3.3 5.5 - - - -
395A ARG* 3.0 30.9 + - - +
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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 GLU* 4.6 10.3 - - + +
8A THR* 1.3 85.5 - - - +
10A ARG* 1.3 62.5 + - - +
11A PRO* 3.3 5.6 - - - +
18A LEU* 3.7 4.6 - - - +
19A TRP* 2.9 53.4 + - + +
21A LEU* 4.7 8.3 - - + -
382A LEU* 3.7 28.3 - - + -
386A ILE* 4.6 7.9 - - + -
387A ARG* 3.6 31.0 - - - +
392A ILE* 3.7 23.6 - - + -
393A ALA 3.8 3.1 - - - -
394A VAL* 3.8 15.7 - - + -
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Residues in contact with ARG 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 71.2 - - - +
11A PRO* 1.3 66.1 - - - +
12A GLU* 3.4 3.1 + - - +
17A LEU 4.2 1.8 - - - +
18A LEU* 3.7 20.4 - - + -
38A ALA* 3.8 35.4 - - + -
39A CYS* 3.7 25.1 - - - +
42A GLU* 2.8 30.7 + - - +
392A ILE* 4.4 1.1 - - - -
393A ALA* 2.9 55.1 + - - +
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Residues in contact with PRO 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* 3.3 12.8 - - + +
10A ARG* 1.3 83.9 - - - +
12A GLU* 1.3 63.7 + - - +
13A GLU 3.3 1.8 - - - +
14A PHE* 3.0 45.3 - - + +
15A PRO* 3.7 3.8 - - - +
17A LEU* 3.6 22.8 - - + +
19A TRP* 3.7 33.2 - - + -
390A LEU* 4.8 8.7 - - + -
391A THR 3.7 6.5 - - - +
392A ILE* 4.2 11.4 - - + -
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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