Contacts of the helix formed by residues 41 - 47 (chain U) 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 ASN 41 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385B ARG* 3.8 15.2 - - - +
189O GLY 4.3 2.6 + - - -
190O LEU* 3.1 40.5 + - + +
213O VAL* 3.8 15.4 - - + +
214O LYS 5.2 3.6 + - - +
40U VAL* 1.3 73.2 - - - +
42U VAL* 1.3 62.7 + - - +
43U VAL* 2.8 20.4 + - - +
44U ASP* 2.8 26.1 + - + +
45U GLU* 3.0 19.2 + - - +
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Residues in contact with VAL 42 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190O LEU* 4.0 17.0 - - + +
214O LYS 5.6 0.2 - - - +
215O ARG* 6.2 2.0 - - - -
216O PHE* 5.4 5.8 - - + +
40U VAL* 3.2 10.5 + - + +
41U ASN* 1.3 70.3 - - - +
43U VAL* 1.3 60.0 + - + +
45U GLU* 3.4 16.5 + - - +
46U LYS* 2.9 29.2 + - - +
118U GLU* 3.7 37.4 - - - +
120U ALA* 3.8 19.1 - - + -
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Residues in contact with VAL 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B ARG* 3.6 31.2 - - + -
190O LEU* 4.3 10.8 - - + +
191O ALA* 4.1 24.2 - - + -
41U ASN* 2.8 15.1 + - - +
42U VAL* 1.3 81.5 - - + +
44U ASP* 1.3 65.0 + - - +
46U LYS* 3.2 14.5 + - - +
47U LEU* 3.2 16.1 + - + +
51U TYR* 5.1 7.0 - - + +
118U GLU* 5.7 0.4 - - + -
120U ALA* 4.6 6.1 - - + -
121U LEU* 4.4 26.0 - - + -
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Residues in contact with ASP 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B PRO* 5.0 3.6 - - - +
385B ARG* 2.8 48.3 + - - +
393B GLU* 2.9 38.7 - - - +
418B LYS* 4.0 16.7 + - - +
195O ASP* 4.2 7.3 - - - +
41U ASN* 2.8 31.0 + - + +
43U VAL* 1.3 73.0 - - - +
45U GLU* 1.3 62.9 + - - +
47U LEU* 3.1 15.0 + - - +
48U GLY 4.1 0.2 + - - -
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Residues in contact with GLU 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B GLU* 5.6 0.7 - - - -
40U VAL* 3.6 29.7 - - + +
41U ASN 3.0 11.8 + - - +
42U VAL* 3.5 18.2 - - - +
44U ASP* 1.3 79.8 - - - +
46U LYS* 1.3 60.9 + - - +
47U LEU 3.1 0.2 - - - -
48U GLY* 3.1 15.8 + - - -
49U THR* 4.0 7.1 - - + +
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Residues in contact with LYS 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42U VAL 2.9 18.2 + - - +
43U VAL* 3.2 8.5 + - - +
45U GLU* 1.3 71.9 - - - +
47U LEU* 1.3 56.1 + - - +
48U GLY 2.9 6.1 + - - -
49U THR* 3.0 37.0 + - + +
51U TYR* 2.9 46.2 - - + +
59U ASN* 2.8 20.4 - - - +
115U THR* 2.9 22.6 - - + +
116U GLU* 2.7 31.6 + - - -
118U GLU* 3.9 16.4 - - + +
121U LEU* 4.4 9.0 - - + -
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Residues in contact with LEU 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B PRO* 5.1 0.4 - - + -
385B ARG* 3.8 30.5 - - + +
388B SER* 3.8 24.2 - - - +
391B SER* 4.0 18.2 - - - +
393B GLU* 3.6 7.7 - - - +
394B GLN* 3.5 36.5 + - - +
43U VAL* 3.2 12.8 + - + +
44U ASP* 3.1 18.8 + - - +
45U GLU 3.1 2.0 - - - -
46U LYS* 1.3 75.2 - - - +
48U GLY* 1.3 55.5 + - - +
49U THR 3.6 0.7 - - - -
51U TYR* 3.7 31.6 - - + -
52U GLY* 4.3 13.4 - - - -
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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