Contacts of the strand formed by residues 68 - 72 (chain D) in PDB entry 3F12
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 68 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D VAL* 4.0 4.9 - - + -
60D TYR* 3.5 23.2 - - + -
64D VAL* 3.0 41.8 + - + +
66D GLY* 5.0 3.5 + - - -
67D ARG* 1.3 121.0 + - + +
69D THR* 1.3 67.2 + - - +
81D LEU* 3.7 20.6 - - + -
82D GLN 3.3 4.9 - - - +
83D MET* 3.3 45.8 - - + -
84D ASN 3.8 9.4 - - - -
86D LEU* 3.8 8.7 - - + -
90D ASP* 4.1 7.4 - - - -
94D TYR* 4.1 11.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D LYS* 5.5 4.7 - - - -
60D TYR* 3.2 10.5 - - - -
66D GLY 6.2 0.4 - - - -
67D ARG 4.7 4.7 - - - +
68D PHE* 1.3 82.3 - - - +
70D ILE* 1.3 65.9 + - - +
71D SER* 3.7 5.7 + - - -
80D TYR 4.4 0.2 - - - -
81D LEU* 3.5 3.1 + - - -
82D GLN* 2.9 43.8 + - + +
84D ASN* 5.0 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D MET 3.9 5.8 - - - +
36D TRP* 3.6 23.1 - - + +
49D ALA* 3.9 5.8 - - + +
50D VAL* 3.6 27.8 - - - +
51D ILE* 3.5 43.3 - - + +
58D LYS* 3.6 31.4 + - + -
60D TYR* 3.1 26.9 + - + +
69D THR* 1.3 77.1 + - - +
71D SER* 1.3 64.9 + - - +
79D LEU* 4.6 3.1 - - + -
80D TYR 3.4 12.8 - - - +
81D LEU* 4.4 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ARG* 4.7 6.3 + - - -
51D ILE* 4.1 6.3 - - - -
69D THR* 4.6 7.4 - - - -
70D ILE* 1.3 76.0 - - - +
72D ARG* 1.3 74.0 + - - +
79D LEU* 3.4 8.0 - - - +
80D TYR* 2.5 67.1 + - - +
82D GLN* 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D PHE* 3.0 9.3 - - + -
51D ILE* 3.5 24.7 - - + +
52D SER 2.4 26.7 + - - -
53D TYR* 2.5 58.7 + - - +
55D GLY* 3.2 29.8 - - - +
71D SER* 1.3 85.5 + - - +
73D ASP* 1.3 61.0 + - - +
74D ASN* 2.7 37.4 + - - +
78D THR 3.8 8.5 - - - +
79D LEU* 4.8 4.0 - - + -
80D TYR* 4.2 3.0 - - - -
----------------------------------------------------------
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