Contacts of the helix formed by residues 18 - 25 (chain K) in PDB entry 2AXT
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 18 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504C BCR 3.5 26.7 - - + -
14K ALA 5.1 0.2 - - - -
15K TYR* 2.6 19.6 + - - +
17K ILE* 1.3 105.7 - - + +
19K ASP* 1.3 69.1 + - - +
20K PRO* 3.2 5.8 - - - -
21K LEU* 2.7 28.7 + - + -
22K VAL* 2.9 25.7 + - + -
6Z GLN* 5.0 5.8 - - + -
9Z LEU* 3.5 37.7 - - + -
10Z ALA* 4.6 14.6 - - + -
13Z VAL* 3.8 21.3 - - + -
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Residues in contact with ASP 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ALA* 4.6 11.8 - - - +
74C HIS* 4.9 0.2 - - - -
11K LEU* 4.6 7.7 - - + +
15K TYR 4.0 2.4 + - - -
16K ALA* 4.0 15.3 + - - +
17K ILE 3.6 0.2 - - - -
18K PHE* 1.3 84.0 - - - +
20K PRO* 1.3 70.6 - - + +
22K VAL* 2.9 8.5 + - - +
23K ASP* 2.8 50.7 + - - +
56K CA 2.8 19.5 - - - -
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Residues in contact with PRO 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K ALA 5.2 0.7 - - - +
17K ILE 4.5 9.6 - - - +
18K PHE* 3.3 6.1 - - - +
19K ASP* 1.3 97.8 - - + +
21K LEU* 1.3 64.5 + - + +
23K ASP* 3.4 21.2 - - - +
24K VAL* 3.5 14.0 - - - +
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Residues in contact with LEU 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C BCR 4.4 12.6 - - + -
18K PHE* 2.7 38.3 + - + +
20K PRO* 1.3 72.6 - - + +
22K VAL* 1.3 56.5 - - - +
23K ASP 3.0 1.6 - - - -
24K VAL* 2.7 31.8 + - + +
25K LEU* 3.3 19.2 + - + +
130X BCR 3.7 48.2 - - + -
13Z VAL* 5.1 4.7 - - + -
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Residues in contact with VAL 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ALA 4.6 1.6 - - - +
69C LEU* 3.7 43.1 - - + +
70C PHE* 4.0 6.2 - - - +
73C ALA* 4.0 6.3 - - + -
504C BCR 4.5 17.7 - - + -
11K LEU* 3.7 29.8 - - + -
18K PHE* 2.9 32.0 + - + +
19K ASP* 3.3 6.7 - - - +
21K LEU* 1.3 72.1 - - - +
23K ASP* 1.3 60.5 + - - +
24K VAL 3.4 0.3 + - - -
25K LEU* 3.8 19.3 + - + +
26K PRO* 3.8 8.8 - - - +
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Residues in contact with ASP 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C PHE* 3.4 26.7 - - + -
73C ALA* 4.5 2.8 - - - +
74C HIS* 3.2 18.6 - - - -
478C UNK 5.5 9.8 - - + +
494C CLA 5.3 3.5 - - - +
19K ASP* 2.8 40.8 + - - +
20K PRO* 3.4 13.9 - - - +
21K LEU 2.9 0.2 + - - -
22K VAL* 1.3 78.4 - - - +
24K VAL* 1.3 61.6 + - + +
26K PRO* 3.8 3.3 - - - +
27K VAL* 5.7 1.2 - - - +
56K CA 2.9 22.7 - - - -
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Residues in contact with VAL 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K PRO 3.5 15.5 - - - +
21K LEU* 2.7 17.4 + - + +
23K ASP* 1.3 73.3 - - + +
25K LEU* 1.3 65.8 + - + +
26K PRO* 3.1 6.0 - - - -
27K VAL* 3.1 25.8 + - + +
28K ILE* 4.1 8.3 + - + +
31K LEU* 6.6 0.2 - - + -
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Residues in contact with LEU 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PHE* 3.6 10.3 - - + -
66C ALA* 3.7 17.0 - - + +
69C LEU* 5.5 4.0 - - + -
119C LEU* 4.1 19.7 - - + -
504C BCR 4.1 26.2 - - + -
21K LEU* 3.3 27.5 + - + +
22K VAL* 4.1 14.1 - - + +
24K VAL* 1.3 76.4 - - + +
26K PRO* 1.3 69.7 - - + +
27K VAL 3.2 0.7 + - - -
28K ILE* 3.2 33.8 + - + +
130X BCR 4.0 28.5 - - + -
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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