Contacts of the helix formed by residues 49 - 60 (chain B) in PDB entry 2AFU
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 49 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE 4.1 1.6 + - - -
48B LEU* 1.3 75.6 - - - +
50B SER* 1.3 65.9 + - - +
51B SER* 3.2 12.5 + - - -
52B ALA* 2.9 30.3 + - - +
53B LEU* 3.0 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ASN* 1.3 74.0 - - - +
51B SER* 1.3 63.8 + - - +
53B LEU* 3.1 6.5 + - - +
54B ARG* 3.1 49.9 + - - +
277B GLU* 4.3 7.8 + - - -
281B LEU* 3.9 24.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ASN* 3.2 11.5 + - - -
50B SER* 1.3 77.9 - - - +
52B ALA* 1.3 62.7 + - - +
54B ARG* 3.3 20.2 + - - +
55B GLN* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.7 30.1 - - + -
49B ASN* 2.9 21.7 + - - +
51B SER* 1.3 72.9 - - - +
53B LEU* 1.3 67.2 + - - +
55B GLN* 3.1 11.8 + - - +
56B ILE* 3.0 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.0 22.4 - - + +
49B ASN 3.0 14.8 + - - +
50B SER* 3.1 10.3 + - - +
52B ALA* 1.3 77.0 - - - +
54B ARG* 1.3 56.2 + - - +
56B ILE* 3.3 5.1 + - - +
57B ALA* 2.9 28.1 + - - +
274B ILE* 5.2 2.0 - - + -
277B GLU* 3.5 33.9 - - + +
278B LEU* 3.9 21.2 - - + +
281B LEU* 3.6 15.7 - - + -
283B LEU* 3.9 3.5 - - + +
353B VAL* 3.7 39.7 - - + -
357B GLU* 4.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B SER* 3.1 28.1 + - - +
51B SER* 3.4 33.3 + - - +
53B LEU* 1.3 72.8 - - - +
55B GLN* 1.3 66.6 + - - +
57B ALA* 3.2 3.2 + - - +
58B GLU* 2.9 35.0 + - + +
281B LEU* 4.2 18.5 + - + +
283B LEU* 3.9 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B SER 3.1 12.0 + - - +
52B ALA* 3.3 13.6 - - - +
54B ARG* 1.3 77.4 - - - +
56B ILE* 1.3 62.9 + - - +
58B GLU* 3.2 7.7 + - - +
59B GLY* 2.8 27.2 + - - -
177B LYS* 3.4 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.8 20.0 - - + -
52B ALA* 3.0 16.1 + - + +
53B LEU* 3.6 6.5 - - - +
55B GLN* 1.3 89.7 - - - +
57B ALA* 1.3 63.6 + - - +
59B GLY* 3.1 12.4 + - - +
60B THR* 3.6 13.7 + - - +
174B LEU* 4.7 5.6 - - + -
177B LYS* 4.5 7.6 - - + -
349B LYS* 4.3 5.4 - - + +
352B GLN* 3.9 29.0 - - + +
353B VAL* 3.8 22.9 - - + +
356B LEU* 3.3 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU 2.9 16.3 + - - +
54B ARG 3.6 4.7 - - - +
56B ILE* 1.3 77.7 - - - +
58B GLU* 1.3 65.6 + - - +
60B THR* 3.8 9.0 - - - +
278B LEU* 5.3 2.4 - - + +
283B LEU* 4.0 29.2 - - + -
349B LYS* 3.3 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ARG* 2.9 32.5 + - + +
55B GLN* 3.7 5.8 - - - +
57B ALA* 1.3 78.9 - - - +
59B GLY* 1.3 63.3 + - - +
60B THR 3.3 6.9 + - - +
283B LEU* 4.1 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLN 2.8 15.9 + - - -
56B ILE* 3.1 5.4 + - - -
58B GLU* 1.3 76.3 - - - +
60B THR* 1.3 56.2 + - - +
172B ARG* 3.4 17.5 + - - -
173B ALA* 3.7 17.0 - - - +
352B GLN* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE 3.6 5.1 + - - +
57B ALA 3.8 17.0 - - - +
58B GLU 3.3 6.5 - - - +
59B GLY* 1.3 78.1 - - - +
61B SER* 1.3 62.1 + - - +
62B ILE 4.0 1.6 + - - -
169B GLU* 2.5 27.4 + - - +
173B ALA* 4.3 0.2 - - - -
345B ASP* 4.4 9.3 + - - +
348B ASN* 4.3 5.6 + - + +
349B LYS* 3.8 29.2 - - + +
352B GLN* 3.1 31.3 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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