Contacts of the strand formed by residues 150 - 155 (chain 4) in PDB entry 1O1F
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 GLY 150 (chain 4).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424 LEU* 3.8 13.9 - - - +
1494 THR* 1.3 78.0 - - - +
1514 ILE* 1.3 61.9 + - - +
1644 PRO* 3.7 0.7 - - - +
1654 ILE* 2.9 28.6 + - - +
2934 LEU* 3.8 12.4 - - - +
2964 ASN* 3.2 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424 LEU* 4.4 0.4 - - - +
1504 GLY* 1.3 74.4 - - - +
1524 VAL* 1.3 65.5 + - - +
1534 LEU 4.0 0.5 + - - -
1624 ASN* 4.5 6.3 - - + +
1634 VAL 3.7 8.5 - - - +
1644 PRO* 3.9 22.9 - - + -
2784 THR* 3.6 30.5 - - + +
2814 SER* 3.6 21.8 - - - +
2824 ILE* 3.7 12.1 - - + -
2934 LEU* 3.4 33.0 - - + +
2964 ASN 2.8 9.3 + - - +
2974 ASN* 3.4 21.3 - - - +
2984 VAL* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1384 ALA* 3.3 41.1 - - + +
1414 SER* 4.3 2.5 - - - -
1424 LEU* 3.8 31.2 - - + +
1514 ILE* 1.3 73.7 - - - +
1534 LEU* 1.3 68.1 + - - +
1544 ASP* 3.6 10.0 + - + -
1614 HIS 4.1 0.2 - - - -
1624 ASN* 3.2 7.2 - - - +
1634 VAL* 2.9 31.1 + - - +
1654 ILE* 4.5 1.6 - - + -
2974 ASN* 5.6 0.2 - - - -
2984 VAL* 3.1 13.7 - - + +
3004 SER* 3.6 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1514 ILE 4.0 1.0 + - - -
1524 VAL* 1.3 71.3 - - - +
1544 ASP* 1.3 59.8 + - - +
1554 SER* 5.1 1.8 - - - -
1604 THR* 4.4 7.9 - - + -
1614 HIS 3.4 8.1 - - - +
1624 ASN* 3.6 24.5 - - - +
2744 ILE* 3.6 41.3 - - + +
2784 THR* 3.9 9.9 - - - +
2974 ASN* 4.5 13.3 - - - +
2984 VAL 2.9 8.0 + - - +
2994 MET* 3.6 34.2 - - + -
3004 SER 3.1 24.3 + - - +
3044 THR* 4.0 13.5 - - + -
3094 ILE* 5.7 5.2 - - + -
3134 MET* 4.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 154 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094 PRO* 5.9 2.3 - - - +
1374 GLN* 4.0 26.2 - - - +
1384 ALA* 4.1 10.6 + - + -
1524 VAL* 3.6 14.0 + - + +
1534 LEU* 1.3 73.6 - - - +
1554 SER* 1.4 64.5 + - - +
1564 GLY 4.4 0.4 + - - -
1594 VAL 4.0 1.5 - - - +
1604 THR* 3.2 4.0 - - - +
1614 HIS* 2.7 50.9 + - + +
1634 VAL* 5.8 0.2 - - + -
3004 SER* 3.0 29.8 + - - +
3014 GLY* 4.0 4.2 + - - -
3394 VAL* 4.2 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1534 LEU* 5.1 3.1 - - - -
1544 ASP* 1.4 76.7 + - - +
1564 GLY* 1.3 61.0 + - - +
1594 VAL 3.6 4.7 + - - -
1604 THR* 2.6 27.2 + - - +
1804 LEU 4.6 0.3 + - - -
1814 ALA* 4.5 2.3 - - - +
2614 LEU* 4.8 4.7 - - - +
2744 ILE* 5.5 1.2 - - - +
3004 SER 3.1 8.3 + - - -
3014 GLY* 3.2 13.7 - - - -
3034 THR* 3.1 38.0 + - - +
3044 THR* 3.6 19.3 - - - -
----------------------------------------------------------
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