Contacts of the strand formed by residues 25 - 31 (chain A) in PDB entry 1XNB
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 ASN 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLY* 2.9 18.9 + - - -
22A SER* 3.0 19.1 + - - +
24A GLY* 1.3 78.5 - - - +
26A TYR* 1.3 67.3 + - - +
27A SER* 5.4 1.0 + - - -
40A LYS* 2.8 24.4 + - - -
181A ASN* 2.9 32.2 + - - +
182A VAL 3.4 7.6 + - - -
183A THR* 3.0 27.8 + - + +
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Residues in contact with TYR 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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6A TRP* 3.5 17.0 - + + -
19A VAL 3.3 15.0 - - - +
21A GLY 4.1 1.1 - - - +
24A GLY 4.4 1.6 - - - -
25A ASN* 1.3 81.9 - - - +
27A SER* 1.3 63.3 + - - +
28A VAL* 4.0 12.6 - - + -
38A VAL* 3.9 25.4 - - + -
39A GLY* 3.7 3.8 - - - -
40A LYS* 3.7 26.2 - - + -
66A LEU* 5.0 0.3 - - - +
169A MET 2.9 29.3 + - - -
170A ALA 3.5 9.5 - - - -
171A THR* 3.4 23.5 + - - -
180A SER* 4.5 1.1 - - - -
181A ASN* 3.4 5.4 - - - +
182A VAL* 2.9 63.3 + - + +
184A VAL* 4.2 6.5 - - + -
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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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17A ASN 4.4 0.9 - - - -
18A ALA* 3.5 0.7 - - - +
19A VAL* 2.8 51.3 + - - +
25A ASN* 5.4 1.0 + - - -
26A TYR* 1.3 79.9 - - - +
28A VAL* 1.3 68.3 + - - +
29A ASN* 5.4 4.7 + - - -
180A SER 3.3 13.9 - - - -
181A ASN* 3.7 19.5 + - - -
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Residues in contact with VAL 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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16A VAL* 4.0 25.6 - - + -
17A ASN 3.3 11.0 - - - +
18A ALA* 4.5 0.7 - - + -
26A TYR* 4.0 8.5 - - + -
27A SER* 1.3 80.8 - - - +
29A ASN* 1.3 71.1 + - - +
30A TRP* 4.0 18.3 - - + -
36A PHE* 4.2 7.9 - - + -
38A VAL* 3.7 30.7 - - + -
171A THR* 4.4 4.9 - - - -
179A SER* 3.3 4.3 - - - -
180A SER* 3.0 46.7 + - - +
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Residues in contact with ASN 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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15A ILE* 4.1 2.7 - - - +
16A VAL 3.7 0.2 - - - -
17A ASN* 2.8 61.0 + - + +
19A VAL* 5.4 2.0 - - - +
27A SER* 5.4 6.1 + - - -
28A VAL* 1.3 77.6 - - - +
30A TRP* 1.3 60.7 + - - +
178A GLY 3.6 5.6 - - - +
179A SER* 3.3 18.6 + - - +
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Residues in contact with TRP 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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15A ILE* 3.2 11.4 - - - +
16A VAL* 4.4 4.5 - - + -
28A VAL* 4.0 15.5 - - + -
29A ASN* 1.3 74.2 - - - +
31A SER* 1.3 63.0 + - - +
33A THR* 3.7 8.5 - - + -
36A PHE* 3.5 35.4 - + + -
58A TRP* 4.3 10.3 - + - -
60A PRO* 4.2 16.2 - - + -
64A GLY* 4.8 9.4 - - - -
171A THR* 3.7 26.7 - - + -
173A GLY* 4.7 0.4 - - - -
176A SER* 3.0 45.2 + - - -
177A SER* 3.2 15.4 - - - -
178A GLY* 2.9 55.5 + - - +
179A SER 3.4 33.2 - - - -
180A SER* 3.9 2.7 - - - -
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Residues in contact with SER 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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14A GLY* 3.6 0.5 - - - -
15A ILE* 2.9 47.0 + - - +
30A TRP* 1.3 78.4 - - - +
32A ASN* 1.3 86.8 + - - +
33A THR* 3.2 3.0 + - - +
177A SER* 3.4 9.0 + - - -
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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