Contacts of the helix formed by residues 52 - 65 (chain L) in PDB entry 1XFB
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 THR 52 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L GLU* 2.9 13.8 + - - +
51L ASN* 1.3 74.4 - - - +
53L GLU* 1.3 75.9 + - + +
54L GLU* 3.2 20.2 - - + +
55L ASN* 3.3 27.1 + - - +
56L ARG* 3.2 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L THR* 1.3 80.3 - - + +
54L GLU* 1.3 58.9 + - - +
56L ARG* 3.1 30.6 + - - +
57L ARG* 2.9 24.3 + - - +
82L GLU* 3.6 12.4 - - + +
86L GLN* 3.5 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L THR* 3.1 14.4 - - + +
53L GLU* 1.3 78.3 - - - +
55L ASN* 1.3 63.2 + - - +
57L ARG* 2.9 36.4 + - - +
58L LEU* 2.7 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 55 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L LEU* 4.4 4.6 - - + +
49L VAL* 3.7 18.7 - - + +
50L GLU* 2.5 44.3 + - - +
52L THR* 3.3 21.9 + - - +
54L GLU* 1.3 79.4 - - - +
56L ARG* 1.3 57.6 + - - +
58L LEU* 3.6 17.9 - - - +
59L TYR* 3.0 22.3 + - - +
314L TRP* 3.5 13.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L VAL* 3.2 35.3 - - - +
40L MET* 3.5 36.6 - - + -
44L LEU* 4.1 5.4 - - + -
51L ASN* 2.8 35.0 + - - +
52L THR 3.2 17.7 + - - +
53L GLU* 3.1 28.6 - - - +
54L GLU 3.0 0.6 - - - -
55L ASN* 1.3 75.8 - - - +
57L ARG* 1.3 67.1 + - - +
59L TYR* 3.1 6.7 + - - +
60L ARG* 2.8 40.4 + - - +
80L PHE* 6.2 0.4 - - - -
82L GLU* 2.8 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L GLU 2.9 8.6 + - - +
54L GLU* 2.9 36.4 + - - +
56L ARG* 1.3 75.0 - - - +
58L LEU* 1.3 86.5 + - - +
60L ARG* 3.4 1.3 + - - -
61L GLN* 2.9 33.2 + - - +
86L GLN* 3.4 35.1 + - + +
87L LYS 3.0 31.9 + - - +
88L ASP* 3.6 9.7 + - - +
89L ASP* 2.9 29.9 + - - +
94L PHE* 3.4 13.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L GLU* 2.7 36.3 + - + +
55L ASN* 3.6 24.0 - - - +
57L ARG* 1.3 98.4 - - - +
59L TYR* 1.3 62.5 + - - +
61L GLN* 3.0 32.5 + - - +
62L VAL* 3.1 12.4 + - - +
89L ASP* 4.4 3.6 - - - +
314L TRP* 4.0 15.5 - - + +
316L GLY 5.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 59 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L MET* 4.6 20.2 - - + -
44L LEU* 4.9 3.8 - - + -
55L ASN 3.0 15.2 + - - +
56L ARG* 3.7 4.7 - - - +
58L LEU* 1.3 77.3 - - - +
60L ARG* 1.3 78.6 + - - +
62L VAL* 2.9 32.7 + - + +
63L LEU* 3.4 22.6 + - + +
307L GLN* 2.7 57.1 + - - +
310L ALA 4.9 1.8 - - - -
311L LEU* 3.3 45.0 - - + +
314L TRP* 3.6 25.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L ALA* 3.1 24.3 + - - +
35L GLU* 2.6 62.4 + - - +
40L MET* 3.5 24.9 - - - +
56L ARG* 2.8 37.7 + - - +
57L ARG 3.8 3.8 - - - +
59L TYR* 1.3 81.7 - - - +
61L GLN* 1.3 56.8 + - - +
63L LEU* 3.1 10.7 + - - +
64L PHE* 2.9 49.3 + - + -
80L PHE* 4.2 5.3 - - - +
82L GLU* 5.1 0.2 + - - -
83L THR* 3.3 29.5 + - + +
86L GLN* 4.2 2.9 - - - +
94L PHE* 4.1 6.5 - - + -
307L GLN* 4.8 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L ARG* 2.9 16.6 + - - +
58L LEU* 3.0 23.8 - - - +
59L TYR 3.0 0.2 - - - -
60L ARG* 1.3 75.7 - - - +
62L VAL* 1.3 54.4 + - - +
64L PHE* 4.4 0.7 - - - +
65L SER* 2.6 46.5 + - - +
88L ASP* 3.0 17.0 - - + +
89L ASP* 2.7 59.2 + - - +
94L PHE* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58L LEU 3.1 14.6 + - - +
59L TYR* 2.9 20.2 + - + +
61L GLN* 1.3 76.4 - - - +
63L LEU* 1.3 65.4 + - + +
65L SER* 3.2 10.5 + - - -
310L ALA* 5.7 0.7 - - + -
314L TRP* 3.9 29.6 - - + +
321L ALA* 3.6 13.0 - - + +
324L ALA* 3.3 31.9 - - + +
325L THR* 2.8 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L LEU* 4.2 19.3 - - + -
33L ALA* 4.4 11.4 - - + -
59L TYR* 3.9 34.1 - - + +
60L ARG* 3.1 10.3 + - - +
61L GLN 3.0 0.6 - - - -
62L VAL* 1.3 78.4 - - + +
64L PHE* 1.3 71.7 + - + +
65L SER 3.1 4.3 - - - -
66L ALA* 3.1 23.9 + - - +
307L GLN* 3.6 38.1 - - + +
310L ALA* 4.6 4.5 - - + -
328L PHE* 3.4 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L LEU* 4.3 11.9 - - + -
33L ALA* 4.4 13.9 - - + -
60L ARG* 2.9 32.9 + - + +
61L GLN 4.2 1.3 - - - +
63L LEU* 1.3 77.0 - - + +
65L SER* 1.3 59.7 + - - +
66L ALA* 3.1 7.0 + - - +
77L VAL* 3.6 26.2 - - + -
79L PHE* 3.7 20.9 - + - -
83L THR* 3.6 28.5 - - + -
94L PHE* 3.3 34.5 - + + -
97L THR* 3.6 23.1 - - + +
98L ILE* 3.5 26.5 - - + +
101L LYS* 4.4 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L GLN* 2.6 31.3 + - - +
62L VAL* 3.2 13.7 + - - -
63L LEU 3.1 0.2 - - - -
64L PHE* 1.3 74.9 - - - +
66L ALA* 1.3 68.7 + - - +
67L ASP* 3.5 2.4 + - - +
97L THR* 5.6 1.6 - - - -
101L LYS* 5.4 0.4 - - - +
325L THR* 3.8 10.6 + - - +
----------------------------------------------------------
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