Contacts of the strand formed by residues 52 - 58 (chain A) in PDB entry 1FO4
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 4.4 3.5 + - - +
49A GLY* 2.6 24.1 + - - -
50A ALA 3.3 1.9 - - - +
51A CYS* 1.3 77.8 - - - +
53A VAL* 1.3 75.7 + - - +
69A SER* 4.0 7.9 - - - -
70A ALA 3.4 6.5 - - - +
71A ASN* 4.3 0.5 + - - -
118A PRO 4.7 0.5 - - - +
119A GLY* 3.6 18.2 - - - +
122A MET* 3.6 23.0 - - + +
123A SER* 3.7 17.7 - - - +
146A ASN* 3.7 0.7 + - - -
341A GLN* 2.8 35.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.9 22.9 - - + -
30A LEU* 4.1 10.3 - - + -
39A THR* 3.9 21.3 - - + +
51A CYS 3.6 9.0 - - - +
52A THR* 1.3 83.3 - - - +
54A MET* 1.3 61.4 + - - +
55A LEU* 4.2 10.8 - - + -
69A SER* 3.3 7.3 - - - -
70A ALA* 3.1 37.4 + - + +
72A ALA* 4.1 8.7 - - + +
85A VAL* 4.2 8.5 - - + -
86A THR 3.6 13.2 - - - +
87A THR* 4.4 5.8 - - + -
122A MET* 4.3 7.4 - - - -
126A THR* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 1.3 74.8 - - - +
55A LEU* 1.3 72.7 + - - +
56A SER* 3.7 17.0 - - - +
67A HIS* 3.9 17.7 - - + +
68A PHE 3.6 10.3 - - - +
85A VAL* 3.4 5.2 - - - +
86A THR* 2.8 49.1 + - - +
122A MET* 4.0 14.4 - - + +
125A TYR* 3.5 32.5 - - + +
126A THR* 3.6 26.9 - - - +
129A ARG* 3.9 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.4 4.0 - - + -
53A VAL* 4.2 7.9 - - + -
54A MET* 1.3 82.2 - - - +
56A SER* 1.3 62.1 + - - +
66A ILE 3.7 0.3 - - - +
67A HIS* 3.4 4.2 - - - -
68A PHE* 2.8 67.6 + - + -
70A ALA* 3.8 24.5 - - + -
75A ALA* 5.6 4.3 - - + -
80A LEU* 4.1 23.1 - - + -
83A VAL* 4.1 12.3 - - + -
84A ALA 3.4 1.6 - - - -
85A VAL* 3.7 30.3 - - + -
345A VAL* 5.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MET* 3.7 13.2 - - - +
55A LEU* 1.3 75.9 - - - +
57A LYS* 1.3 65.5 + - - +
65A ILE* 4.3 0.2 - - - -
66A ILE 3.2 5.4 - - - -
67A HIS* 2.5 36.1 + - - -
83A VAL* 3.5 2.9 - - - +
84A ALA* 2.7 41.1 + - - +
86A THR* 5.0 2.1 + - - -
212A PHE* 3.8 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 1.3 77.3 - - - +
58A TYR* 1.3 72.9 + - - +
59A ASP* 5.4 2.7 - - - +
65A ILE* 3.3 3.9 - - - +
66A ILE* 2.9 55.2 + - + +
68A PHE* 3.7 25.1 - - + -
82A HIS 4.4 13.0 - - - +
83A VAL* 4.4 20.2 - - + +
212A PHE* 3.8 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 1.3 85.2 - - - +
59A ASP* 1.3 59.7 + - - +
60A ARG* 3.5 58.1 + - + +
63A ASP* 2.6 51.4 + - - +
64A LYS* 4.0 3.8 - - - -
65A ILE* 3.7 23.6 - - + -
82A HIS 5.5 0.6 + - - -
212A PHE* 4.0 9.8 - - + -
216A LEU 5.6 1.1 - - - +
217A LEU* 4.5 2.9 - - + -
220A LYS* 3.7 50.0 + - + +
----------------------------------------------------------
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