Contacts of the strand formed by residues 23 - 28 (chain A) in PDB entry 1A16
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 SER 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A MET* 3.3 17.8 - - - +
20A GLN 2.6 25.4 + - - -
22A GLY* 1.3 79.5 - - - +
24A ALA* 1.3 62.7 + - - +
65A ILE* 3.5 1.9 - - - +
66A LYS* 2.8 28.8 + - - +
124A LEU* 3.7 9.5 - - - +
126A VAL* 3.2 22.9 - - - -
128A TYR* 3.3 18.5 - - - -
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A MET* 4.1 3.4 - - - -
23A SER* 1.3 77.6 - - - +
25A ALA* 1.3 54.4 + - - +
26A LEU* 4.6 0.9 - - + -
63A VAL* 4.5 7.4 - - + -
64A LEU 3.1 9.9 - - - +
65A ILE* 4.2 12.3 - - + -
120A LEU 5.0 0.7 - - - +
121A LEU* 3.8 19.1 - - + -
124A LEU* 3.4 20.6 - - + -
126A VAL 3.1 5.8 + - - +
127A VAL* 3.3 5.9 - - - +
128A TYR* 2.8 31.3 + - - +
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Residues in contact with ALA 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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15A LEU* 4.3 16.2 - - + -
19A MET* 3.8 24.8 - - - +
24A ALA* 1.3 72.5 - - - +
26A LEU* 1.3 62.6 + - - +
27A ILE* 4.8 3.3 - - + +
62A LEU 3.3 1.6 - - - +
63A VAL* 3.3 6.1 - - - -
64A LEU* 2.7 42.1 + - + +
128A TYR* 3.5 17.9 - - + -
165A TRP* 4.8 4.5 - - + -
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Residues in contact with LEU 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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24A ALA* 4.6 2.5 - - + -
25A ALA* 1.3 80.3 - - - +
27A ILE* 1.3 62.2 + - - +
28A PHE* 4.0 20.8 + - + -
61A VAL* 4.8 2.2 - - + -
62A LEU 3.5 3.1 - - - +
63A VAL* 3.8 30.1 - - + -
117A LEU* 4.1 24.9 - - + -
121A LEU* 4.4 13.0 - - + -
127A VAL* 3.9 22.2 - - + -
128A TYR 2.9 17.7 + - - +
129A HIS* 4.4 6.7 + - + +
130A ALA 4.7 0.2 + - - -
141A VAL* 3.7 29.2 - - + -
165A TRP* 2.8 24.6 + - - +
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Residues in contact with ILE 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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15A LEU* 4.2 16.2 - - + -
25A ALA* 4.8 2.2 - - + -
26A LEU* 1.3 80.6 - - - +
28A PHE* 1.3 63.2 + - - +
46A ASN* 5.1 0.7 - - - +
48A ASP 4.1 3.4 - - - +
49A PHE* 3.2 40.9 - - + +
52A PHE* 3.4 35.0 - - + -
61A VAL* 3.4 1.7 - - - +
62A LEU* 2.7 58.5 + - + +
64A LEU* 4.7 5.2 - - + -
165A TRP* 3.9 28.9 - - + +
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Residues in contact with PHE 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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26A LEU* 4.0 24.5 - - + -
27A ILE* 1.3 77.6 - - - +
29A ALA* 1.3 63.0 + - - +
46A ASN* 3.9 10.9 + - - +
49A PHE* 3.5 15.9 - - - +
60A ALA 3.8 2.2 - - - -
61A VAL* 3.2 37.0 - - + -
113A ILE* 5.0 0.4 - - + -
117A LEU* 5.2 1.3 - - + -
129A HIS* 4.0 7.4 - + - -
134A TYR* 4.1 9.2 - - + -
136A TYR* 3.6 17.9 - + + +
137A ALA* 3.6 39.7 - - + -
140A ILE* 4.0 24.5 - - + -
141A VAL* 3.7 31.6 - - + -
165A TRP* 5.3 1.6 - - - -
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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