Contacts of the strand formed by residues 20 - 31 (chain A) in PDB entry 1GAJ
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 PHE 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TYR* 3.5 3.5 - - - -
17A PHE* 2.9 47.1 + + + +
19A GLU* 1.3 79.1 - - - +
21A LYS* 1.3 65.3 + - - +
22A ALA* 3.5 34.6 + - + -
43A GLY* 4.9 12.8 - - - -
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Residues in contact with LYS 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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14A VAL* 3.5 28.0 - - + +
15A LYS 4.0 5.6 - - - +
16A TYR* 3.9 31.6 + - + -
19A GLU 3.5 2.3 + - - +
20A PHE* 1.3 82.9 - - - +
22A ALA* 1.3 62.7 + - - +
23A LEU 3.1 19.5 + - - +
24A ASP* 3.3 41.1 + - - +
228A ASN 4.6 9.4 - - - +
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Residues in contact with ALA 22 (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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15A LYS 3.3 8.7 + - - +
17A PHE* 3.5 37.2 - - + -
20A PHE* 3.5 24.1 + - + -
21A LYS* 1.3 72.6 - - - +
23A LEU* 1.3 64.2 + - - +
43A GLY 5.5 0.5 - - - +
45A GLY* 3.7 11.7 + - - -
48A THR* 4.2 14.8 - - + +
228A ASN 4.6 0.4 - - - -
229A GLY* 3.2 18.5 + - - -
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Residues in contact with LEU 23 (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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13A ILE* 3.5 35.2 - - + +
14A VAL* 3.8 3.6 - - - +
15A LYS* 3.4 27.6 + - + +
21A LYS* 3.1 24.0 - - - +
22A ALA* 1.3 83.8 - - - +
24A ASP* 1.3 61.1 + - - +
25A GLY 4.1 0.9 - - - -
26A VAL* 4.3 6.1 - - + -
45A GLY 3.2 26.9 - - - +
48A THR* 4.1 10.5 - - + -
49A LEU* 3.6 30.1 - - + +
52A VAL* 4.2 6.3 - - + -
226A MET* 4.1 11.7 - - + -
229A GLY* 3.5 5.8 - - - +
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Residues in contact with ASP 24 (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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13A ILE 4.1 0.2 + - - -
21A LYS* 3.3 38.5 + - + +
23A LEU* 1.3 74.5 - - - +
25A GLY* 1.3 69.4 + - - +
26A VAL* 3.4 0.6 - - - +
228A ASN 4.4 7.2 - - - +
229A GLY 2.7 20.7 + - - +
230A GLN* 3.7 33.3 + - + +
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Residues in contact with GLY 25 (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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12A ASN* 3.7 34.8 - - - +
13A ILE 3.1 12.4 + - - -
14A VAL* 3.6 12.2 - - - +
24A ASP* 1.3 75.0 + - - +
26A VAL* 1.3 62.9 + - - +
27A SER* 3.6 2.9 + - - -
230A GLN* 5.4 1.0 - - - +
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Residues in contact with VAL 26 (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 THR* 2.8 13.5 + - - +
12A ASN 3.5 0.7 + - - -
13A ILE* 2.9 31.4 + - + +
23A LEU* 4.3 11.9 - - + -
24A ASP 4.2 2.7 - - - +
25A GLY* 1.3 76.2 - - - +
27A SER* 1.3 63.1 + - - +
28A ILE* 4.0 12.3 - - + -
49A LEU* 4.0 25.1 - - + -
226A MET* 4.8 3.1 - - + -
229A GLY 2.8 31.2 - - - +
230A GLN* 3.7 13.0 - - - -
231A ILE* 3.7 24.2 - - + +
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Residues in contact with SER 27 (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 THR 2.9 15.5 - - - -
11A GLU* 3.7 1.6 - - - -
12A ASN* 2.8 35.0 + - - -
25A GLY 3.6 3.2 + - - -
26A VAL* 1.3 73.2 - - - +
28A ILE* 1.3 68.5 + - - +
224A TYR* 4.7 3.1 - - - -
231A ILE* 4.0 10.2 - - - +
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Residues in contact with ILE 28 (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 LEU* 5.0 3.1 - - + -
9A ARG* 2.8 28.3 - - - +
10A THR* 2.9 22.7 + - + +
26A VAL* 4.0 6.5 - - + -
27A SER* 1.3 81.3 - - - +
29A SER* 1.3 60.7 + - - +
30A VAL* 4.7 15.3 - - + -
38A ILE* 4.2 12.3 - - + -
49A LEU* 4.2 15.5 - - + -
53A ILE* 4.2 22.9 - - + -
207A LEU* 4.8 5.4 - - + -
224A TYR* 3.4 33.0 - - + -
231A ILE* 3.9 20.4 - - + -
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Residues in contact with SER 29 (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 GLU* 2.7 38.2 + - - +
8A LEU 3.2 4.7 - - - -
9A ARG* 4.6 0.7 - - - -
28A ILE* 1.3 73.8 - - - +
30A VAL* 1.3 64.3 + - - +
31A ASN* 4.3 3.7 + - - -
222A HIS* 3.1 17.0 + - - -
224A TYR* 2.9 18.8 + - - -
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Residues in contact with VAL 30 (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 GLU* 3.6 1.4 - - - -
7A ILE* 2.8 31.5 + - + +
8A LEU* 2.7 40.2 + - + +
28A ILE* 4.7 9.4 - - + -
29A SER* 1.3 80.7 + - - +
31A ASN* 1.3 66.9 + - - +
34A ASP* 4.5 0.4 - - + -
36A THR* 3.1 39.9 - - + +
174A MET* 4.6 5.6 - - + -
205A THR* 3.8 16.8 - - + -
206A PHE 4.5 3.4 - - - +
207A LEU* 4.7 9.9 - - + -
222A HIS* 4.9 1.8 - - - -
224A TYR* 5.0 0.4 - - + -
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Residues in contact with ASN 31 (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 MET* 3.0 33.6 + - + +
6A GLU* 3.4 10.7 - - - +
7A ILE* 4.1 1.1 - - - -
29A SER* 5.0 3.5 + - - -
30A VAL* 1.3 74.9 - - - +
32A LYS* 1.3 69.4 + - - +
34A ASP* 2.9 38.6 + - - +
205A THR* 3.2 7.4 - - - +
222A HIS* 5.5 4.3 - - - -
236A ARG* 3.4 36.6 + - - +
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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