Contacts of the strand formed by residues 15 - 22 (chain A) in PDB entry 2ANL
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 MET 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASP* 4.4 2.0 - - - -
11A VAL* 2.7 41.0 + - + +
13A ASN* 3.8 3.8 - - + +
14A LEU* 1.3 78.6 - - - +
16A PHE* 1.3 104.5 + - + +
32A ILE* 4.4 20.0 - - + -
215A SER 3.5 7.2 - - - +
216A GLY* 3.3 30.5 - - - +
217A THR 4.6 2.2 - - - -
218A SER* 4.8 7.0 - - - -
303A ASP* 3.5 21.1 - - - +
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Residues in contact with PHE 16 (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* 3.8 29.6 - - + -
9A ASP 3.5 17.9 - - - +
10A ASP* 4.0 7.4 - - + +
11A VAL* 5.0 0.4 - - - -
14A LEU 5.5 1.6 - - - -
15A MET* 1.3 106.3 - - + +
17A TYR* 1.3 58.0 + - - +
32A ILE* 4.5 6.9 - - - +
33A PHE 4.1 10.3 - - - -
156A PHE* 3.9 29.8 - + - -
158A LEU* 3.5 44.0 - - + -
166A GLY* 5.9 0.4 - - - -
215A SER* 3.2 23.3 - - - -
303A ASP* 3.9 14.6 - - - -
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Residues in contact with TYR 17 (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* 3.3 12.0 - - - -
9A ASP* 3.0 73.4 + - + +
10A ASP 5.3 0.2 - - - -
11A VAL* 4.4 20.9 - - + -
16A PHE* 1.3 74.7 - - - +
18A GLY* 1.3 82.3 + - - +
19A GLU* 4.5 5.8 - - + -
30A MET* 3.3 53.7 - - + +
31A LEU 3.8 18.8 - - - +
32A ILE* 5.0 1.3 - - + +
33A PHE* 4.8 0.9 - - - -
119A GLU 4.1 13.0 - - - +
120A PHE* 5.2 1.6 - - + -
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Residues in contact with GLY 18 (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* 5.1 1.6 - - - -
7A GLU 3.8 12.3 - - - -
8A LEU* 4.7 2.5 - - - -
9A ASP* 5.8 0.2 - - - -
17A TYR* 1.3 84.0 - - - +
19A GLU* 1.3 68.3 + - - +
29A PHE 3.3 1.2 - - - +
30A MET* 3.5 2.3 - - - -
31A LEU 3.1 22.8 + - - +
33A PHE* 3.6 23.2 - - - -
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Residues in contact with GLU 19 (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* 4.5 8.8 - - + +
7A GLU 4.4 5.3 + - - -
9A ASP* 5.9 0.2 + - - -
17A TYR* 4.4 8.2 - - + -
18A GLY* 1.3 75.9 - - - -
20A GLY* 1.3 58.9 + - - +
21A GLU* 4.0 14.4 - - - +
28A LYS* 3.2 54.6 + - + +
29A PHE 3.5 6.5 - - - +
30A MET* 5.0 1.3 - - + +
33A PHE* 3.9 14.0 - - - -
93A LEU* 5.4 4.3 - - - +
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Residues in contact with GLY 20 (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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19A GLU* 1.3 78.9 - - - +
21A GLU* 1.3 62.9 + - - -
22A VAL* 5.4 1.1 - - - -
27A GLN 3.4 0.2 - - - +
28A LYS* 3.3 0.8 - - - -
29A PHE* 2.5 51.2 + - - +
31A LEU* 4.2 17.9 - - - -
92A THR 4.4 5.6 - - - -
93A LEU* 5.0 3.4 - - - -
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Residues in contact with GLU 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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19A GLU* 4.0 17.4 - - - +
20A GLY* 1.3 76.5 - - - -
22A VAL* 1.3 59.3 - - - +
26A HIS* 2.9 51.0 - - + +
27A GLN 2.8 16.2 - - - +
28A LYS* 3.6 17.1 - - + +
91A VAL* 3.7 3.3 - - - +
92A THR* 2.8 54.0 + - + +
93A LEU* 4.9 0.2 - - - +
94A GLY* 5.2 8.9 + - - +
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Residues in contact with VAL 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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20A GLY 5.1 0.9 - - - +
21A GLU* 1.3 77.1 - - - +
23A GLY* 1.3 62.4 + - - +
25A ASN* 3.8 3.8 - - - +
27A GLN* 3.0 24.3 + - + +
29A PHE* 4.3 18.8 - - + -
40A LEU* 5.9 1.6 - - + -
42A VAL* 4.3 19.5 - - + -
58A TYR* 2.9 43.5 - - + -
89A ASP* 4.8 1.1 - - - +
90A LEU 2.9 9.4 - - - +
91A VAL* 4.4 15.0 - - + +
102A PHE* 5.0 9.4 - - + -
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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