Contacts of the helix formed by residues 47 - 59 (chain B) in PDB entry 1CCW
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 47 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU 5.5 4.4 + - - -
42B ILE* 4.9 5.5 - - + +
43B PRO 3.4 6.6 + - - +
44B ALA* 3.0 12.6 + - - +
46B LYS* 1.3 78.8 - - - +
48B PHE* 1.3 59.2 + - - +
49B ALA* 2.9 14.0 + - - +
50B GLU* 2.9 50.4 + - - +
51B LYS* 2.9 28.4 + - - +
145B PRO* 3.8 1.3 - - - -
168B THR* 3.5 18.1 - - + +
209B VAL* 5.4 2.8 - - - +
210B HIS* 3.0 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASN* 1.3 71.5 + - - +
49B ALA* 1.3 64.9 + - - +
51B LYS* 3.4 1.4 + - - +
52B LEU* 3.0 43.6 + - + +
64B GLN* 3.7 3.8 - - - -
90B PHE* 3.3 48.9 - + + -
145B PRO* 3.5 28.1 - - + +
146B LEU 4.0 6.5 - - - -
147B GLN* 3.5 36.1 - - + -
168B THR* 2.8 29.5 + - - +
169B SER* 3.7 16.4 - - - -
212B ASN* 4.2 4.3 - - + -
322B LYS* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASN* 2.9 8.6 + - - +
48B PHE* 1.3 80.2 - - - +
50B GLU* 1.3 61.8 + - - +
52B LEU* 3.4 2.8 + - - +
53B VAL* 3.2 19.5 + - - +
168B THR 4.3 1.2 + - - -
210B HIS* 3.9 31.2 - - + +
211B ILE 4.1 0.7 - - - +
212B ASN* 4.1 10.6 - - - +
247B ASN* 3.3 40.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA* 3.2 37.0 - - + +
47B ASN* 2.9 32.0 + - + +
49B ALA* 1.3 77.3 - - - +
51B LYS* 1.3 62.8 + - - +
53B VAL* 3.2 12.0 + - + +
54B LEU* 3.1 19.6 + - - +
210B HIS* 3.4 30.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA 4.5 5.3 + - - +
45B GLU* 4.3 8.5 + - - +
47B ASN 2.9 17.7 + - - +
49B ALA 3.4 0.2 - - - -
50B GLU* 1.3 76.5 - - - +
52B LEU* 1.3 57.3 + - - +
54B LEU* 3.2 16.9 + - + +
55B ALA* 2.9 27.2 + - - +
62B MET* 3.9 26.7 - - + -
89B ASP* 2.8 30.8 + - - +
90B PHE* 3.7 27.8 - - + -
144B LEU* 3.5 18.8 - - - +
145B PRO* 3.9 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 3.0 30.3 + - + +
49B ALA 3.6 4.9 - - - +
50B GLU 3.2 0.2 - - - -
51B LYS* 1.3 77.9 - - - +
53B VAL* 1.3 61.8 + - + +
55B ALA* 3.3 4.8 + - + +
56B LYS* 3.0 25.6 + - - +
90B PHE* 3.8 23.3 - - + -
212B ASN* 3.3 37.9 - - - +
247B ASN* 3.7 9.6 - - - +
249B THR* 3.3 13.0 - - + +
287B THR* 3.9 21.3 - - + +
321B THR* 4.1 19.6 - - + +
322B LYS* 4.7 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA 3.2 15.0 + - - +
50B GLU* 3.2 11.1 + - + +
52B LEU* 1.3 76.4 - - - +
54B LEU* 1.3 58.9 + - - +
56B LYS* 3.3 3.5 + - - +
57B LYS* 3.0 29.8 + - + +
247B ASN* 4.1 5.2 - - - +
285B PHE* 3.9 43.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU 3.1 10.6 + - - +
51B LYS* 3.4 24.9 - - + +
52B LEU 3.2 0.2 - - - -
53B VAL* 1.3 80.4 - - - +
55B ALA* 1.3 63.9 + - - +
57B LYS* 3.2 16.7 + - + +
58B LYS* 2.9 62.1 + - + +
60B ILE* 5.8 0.2 - - + -
62B MET* 5.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LYS 2.9 12.3 + - - +
52B LEU* 3.3 6.7 + - + +
54B LEU* 1.3 77.0 - - - +
56B LYS* 1.3 59.2 + - - +
58B LYS* 3.3 0.8 + - - -
59B GLY* 2.9 24.9 + - - -
60B ILE* 3.2 23.9 + - - +
62B MET* 3.5 40.4 - - + -
321B THR* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU 3.0 8.4 + - - +
53B VAL 3.5 7.9 - - - +
55B ALA* 1.3 78.1 - - - +
57B LYS* 1.3 62.2 + - - +
59B GLY* 3.3 12.3 + - - -
269B GLU* 2.7 36.0 + - - -
285B PHE* 3.9 18.8 - - + -
286B VAL 3.8 12.8 - - - -
287B THR* 3.7 20.4 - - + +
288B THR* 5.3 0.6 + - - -
319B GLY 4.7 9.5 + - - -
321B THR* 3.8 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 3.0 16.6 + - + +
54B LEU* 3.4 22.2 - - + +
56B LYS* 1.3 77.5 - - - +
58B LYS* 1.3 63.8 + - + +
59B GLY 3.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 2.9 47.2 + - + +
55B ALA 4.0 0.4 - - - +
57B LYS* 1.3 85.5 - - + +
59B GLY* 1.3 61.7 + - - +
60B ILE* 3.4 35.4 + - + +
----------------------------------------------------------
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 ALA 2.9 7.0 + - - -
56B LYS* 3.3 10.9 + - - -
57B LYS 3.5 0.4 + - - -
58B LYS* 1.3 79.3 - - - +
60B ILE* 1.3 58.0 + - - +
356B GLY* 5.1 6.1 + - - -
358B ARG* 2.7 33.4 + - - -
----------------------------------------------------------
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