Contacts of the strand formed by residues 52 - 62 (chain G) in PDB entry 1I5L
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 GLU 52 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE* 3.4 5.2 - - - -
49G GLN 2.9 31.6 + - - +
50G ASN 3.2 6.2 + - - +
51G GLY* 1.3 80.1 - - - +
53G VAL* 1.3 75.3 + - - +
54G VAL* 3.5 10.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G GLU* 4.2 30.5 - - + +
47G GLU 3.3 6.5 - - - +
48G ILE* 4.5 11.7 - - + -
51G GLY 4.2 2.2 + - - +
52G GLU* 1.3 82.8 - - - +
54G VAL* 1.3 61.7 + - - +
55G ARG* 3.6 25.1 - - - +
56G LYS* 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ARG* 4.7 13.5 - - - +
47G GLU* 2.8 23.4 + - + +
48G ILE 5.0 0.2 - - - -
49G GLN* 4.1 26.9 - - + +
52G GLU* 3.6 20.0 - - + +
53G VAL* 1.3 72.8 - - - +
55G ARG* 1.3 76.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ILE* 3.9 27.4 - - - +
26F GLU* 3.6 34.6 + - - -
51F GLY* 5.6 7.3 - - - -
69F PHE* 5.2 12.3 - - - -
27G PHE* 6.5 0.4 - - + -
46G GLU* 2.9 6.8 - - - +
47G GLU* 2.6 53.8 + - + +
53G VAL* 3.5 7.3 - - - +
54G VAL* 1.3 91.1 + - - +
56G LYS* 1.3 75.6 + - - +
57G VAL* 3.8 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F PRO* 6.2 0.2 - - - +
45G ALA 3.3 4.7 - - - +
46G GLU* 3.2 35.0 + - + -
53G VAL* 4.6 8.7 - - + -
55G ARG* 1.3 79.7 - - - +
57G VAL* 1.3 69.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ILE* 6.1 2.5 - - + -
69F PHE* 6.1 1.1 - - + -
71F SER* 3.9 18.8 - - - +
72F PRO 5.5 4.0 - - - +
74F PRO* 5.9 5.4 - - + -
27G PHE* 4.4 8.3 - - + -
44G ASP* 3.4 3.3 - - - -
45G ALA* 2.8 51.5 + - + +
47G GLU 5.9 0.2 - - - +
55G ARG* 3.8 23.6 - - + +
56G LYS* 1.3 81.5 - - - +
58G GLY* 1.3 67.0 + - - +
59G SER 4.1 9.4 - - - +
60G VAL* 3.4 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F PRO* 5.5 2.8 + - - -
74F PRO* 5.1 12.2 - - - +
43G LEU* 3.4 4.2 - - - +
44G ASP* 2.5 36.2 + - - +
57G VAL* 1.3 71.7 - - - +
59G SER* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F VAL* 5.2 9.1 - - - +
71F SER* 3.1 22.3 - - - -
72F PRO* 3.2 28.2 - - - +
41G VAL* 5.5 3.6 - - - -
42G LEU 2.9 17.3 - - - -
43G LEU* 3.4 19.6 - - - +
45G ALA 5.5 0.2 - - - +
57G VAL* 3.2 3.9 - - - +
58G GLY* 1.3 81.9 - - - +
60G VAL* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F VAL* 6.2 0.2 - - - -
69F PHE* 4.5 8.3 - - + -
70F VAL 3.6 4.7 - - - +
71F SER* 3.3 18.8 - - - +
72F PRO* 5.2 0.2 - - - -
27G PHE* 3.9 25.6 - - + -
40G LEU 3.7 0.9 - - - +
41G VAL* 3.3 8.0 - - - +
42G LEU* 2.8 70.9 + - + +
45G ALA* 4.5 1.6 - - + -
57G VAL* 3.4 20.4 - - + -
59G SER* 1.3 80.7 - - - +
61G VAL* 1.3 68.0 + - - +
62G ILE* 4.0 7.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F PRO* 4.3 26.0 - - + +
8F VAL* 4.1 30.1 - - + -
9F LEU* 4.7 17.7 - - + -
38F MET* 5.1 15.7 - - + +
67F VAL* 5.7 0.2 - - - +
69F PHE* 3.1 6.3 - - - -
70F VAL* 2.8 47.2 + - + +
72F PRO* 6.2 1.8 - - + -
39G ASN* 5.4 1.6 - - + -
40G LEU 3.4 9.6 - - - +
41G VAL* 4.8 3.8 - - + -
60G VAL* 1.3 78.0 - - - +
62G ILE* 1.3 65.0 + - - +
63G ARG* 4.0 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F VAL 3.7 9.2 - - - +
69F PHE* 4.2 11.2 - - + -
19G VAL* 4.1 16.6 - - + -
21G LEU* 4.0 15.9 - - + -
27G PHE* 3.9 24.2 - - + -
38G MET 4.4 0.2 - - - +
39G ASN* 3.2 5.4 - - - +
40G LEU* 3.0 39.4 + - + +
42G LEU* 3.8 29.8 - - + -
60G VAL* 4.6 8.7 - - + +
61G VAL* 1.3 76.7 - - - +
63G ARG* 1.3 75.6 + - - +
64G GLY* 4.2 0.2 - - - -
66G THR* 4.5 0.9 - - - -
67G VAL* 4.0 16.6 - - + -
----------------------------------------------------------
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