Contacts of the strand formed by residues 8 - 15 (chain A) in PDB entry 1AIS
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 LYS 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LYS 3.6 3.8 + - - +
7A VAL* 1.3 75.8 - - - +
9A LEU* 1.3 74.7 + - - +
10A ARG* 5.7 3.1 - - + -
109A GLY* 2.9 5.4 - - - -
110A ASP* 2.8 44.4 + - + +
168A TRP* 5.7 0.2 - - - +
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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 VAL* 4.3 6.7 - - + -
8A LYS* 1.3 92.6 - - - +
10A ARG* 1.3 61.1 + - - +
107A PHE* 4.0 31.4 - - + -
108A SER 3.5 11.4 - - - +
109A GLY* 4.1 0.4 - - - -
156A ILE* 4.0 25.8 - - + -
158A CYS* 5.2 3.1 - - + -
164A GLU 5.2 0.7 - - - +
167A ALA* 4.1 19.3 - - + -
168A TRP* 3.6 35.8 - - + +
171A VAL* 4.2 14.8 - - + -
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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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8A LYS* 5.7 4.0 - - + -
9A LEU* 1.3 75.3 - - - +
11A ILE* 1.3 71.5 + - - +
12A GLU* 3.4 24.2 + - - +
107A PHE* 3.1 7.7 - - - -
108A SER* 2.8 42.5 + - - +
109A GLY* 5.6 0.7 - - - -
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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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10A ARG* 1.3 81.6 + - - +
12A GLU* 1.3 66.6 + - - +
13A ASN 3.9 8.5 - - - +
14A ILE* 3.6 25.6 - - + -
71A LYS* 3.6 36.2 - - - +
72A SER* 5.6 1.1 - - - -
105A MET* 3.7 21.1 - - + -
106A VAL 3.9 4.7 - - - +
107A PHE* 3.5 23.3 - - + -
164A GLU* 4.0 20.2 - - - +
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Residues in contact with GLU 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 ARG* 3.4 25.1 + - - +
11A ILE* 1.3 81.5 - - - +
13A ASN* 1.3 63.9 + - + +
69A GLY 4.9 0.5 - - - +
71A LYS* 2.9 45.0 + - - +
106A VAL* 2.8 14.8 + - + +
107A PHE 4.3 0.4 - - - -
108A SER* 2.6 38.0 + - - +
1424E A 3.3 15.4 - - - +
1425E A 3.3 41.7 - - - +
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Residues in contact with ASN 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 ILE* 3.8 2.2 - - - +
12A GLU* 1.3 82.9 - - - +
14A ILE* 1.3 71.6 + - - +
15A VAL* 3.8 10.1 - - - +
69A GLY* 2.8 31.9 + - - -
70A ALA 3.4 6.3 - - - -
104A ASN 4.8 0.2 - - - -
105A MET* 3.5 2.6 - - - -
106A VAL* 2.9 35.5 + - + +
1423E A 3.1 34.2 + - - -
1424E A 3.3 36.5 + - - +
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Residues in contact with ILE 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 ILE* 3.6 18.4 - - + -
13A ASN* 1.3 87.0 + - - +
15A VAL* 1.3 63.9 + - - +
16A ALA 4.2 0.4 + - - -
67A VAL 3.7 6.6 - - - +
68A THR* 3.8 1.0 - - - -
70A ALA* 2.8 34.4 + - + +
72A SER* 3.7 35.4 - - - +
73A VAL* 4.1 8.3 - - + +
76A ILE* 3.7 18.7 - - + +
102A VAL* 3.9 27.4 - - + -
104A ASN 3.6 4.3 - - - +
105A MET* 3.9 22.9 - - + -
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Residues in contact with VAL 15 (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 ASN* 3.8 7.0 - - - +
14A ILE* 1.3 75.6 - - - +
16A ALA* 1.3 58.1 + - - +
66A VAL* 4.0 7.4 - - + -
67A VAL 3.3 2.9 - - - -
68A THR* 3.2 30.1 - - + -
102A VAL* 3.6 3.6 - - - +
103A GLN* 2.7 36.6 + - + -
104A ASN* 2.8 31.3 + - + +
1412C 5IU 3.5 26.2 - - + +
1413C A 3.8 18.8 - - + +
1423E A 3.7 7.2 - - + -
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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