Contacts of the strand formed by residues 999 - 1007 (chain T) in PDB entry 3F5P
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 ILE 999 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994T VAL* 4.3 11.0 - - + -
995T ALA 3.9 10.1 - - - +
996T ARG* 2.5 28.1 + - - +
997T GLU 3.2 2.0 + - - -
998T LYS* 1.3 85.7 - - - +
1000T THR* 1.3 66.7 + - - +
1001T MET* 4.3 5.1 + - + +
1017T VAL 3.5 1.3 - - - -
1018T ALA* 3.5 24.7 - - + -
1021T VAL* 4.6 2.0 - - + -
1032T ILE* 3.7 27.4 - - + -
1069T VAL* 3.9 16.6 - - + -
1076T LEU* 3.9 21.0 - - + +
1078T ILE* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1000 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997T GLU 5.4 4.7 - - - +
998T LYS 4.3 0.2 - - - -
999T ILE* 1.3 78.7 - - - +
1001T MET* 1.3 65.0 + - - +
1002T SER* 5.4 0.2 - - - -
1016T GLY* 3.2 3.3 - - - -
1017T VAL* 2.9 56.4 + - - +
1019T LYS* 5.3 7.2 - - + +
1032T ILE* 5.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1001 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999T ILE* 4.3 7.4 + - + +
1000T THR* 1.3 76.7 - - - +
1002T SER* 1.3 63.7 + - - +
1014T TYR* 4.2 32.3 - - + -
1015T GLU 3.7 4.7 - - - +
1032T ILE* 4.0 31.9 - - + -
1034T THR* 3.6 32.5 - - + -
1076T LEU* 4.6 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1002 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000T THR 4.0 1.2 + - - -
1001T MET* 1.3 75.6 - - - +
1003T ARG* 1.3 81.6 + - - +
1004T GLU* 5.5 0.5 - - - +
1014T TYR* 4.8 4.8 - - - -
1015T GLU* 2.9 27.6 + - - +
1016T GLY* 4.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1003 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002T SER* 1.3 96.0 + - - +
1004T GLU* 1.3 78.7 + - + +
1005T LEU* 4.4 10.2 - - - +
1014T TYR* 3.8 5.4 - - - -
1015T GLU* 2.9 46.0 + - + +
1029T ARG* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1004 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002T SER 5.5 0.3 - - - +
1003T ARG* 1.3 91.2 - - + +
1005T LEU* 1.3 60.5 + - - +
1006T GLY* 4.5 1.8 - - - +
1012T MET* 4.2 25.1 - - + +
1013T VAL 3.6 10.1 - - - +
1014T TYR* 2.7 39.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1005 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16T 741 3.5 71.9 - - + +
1003T ARG* 4.4 10.3 - - - +
1004T GLU* 1.3 77.5 - - - +
1006T GLY* 1.3 59.4 + - - +
1013T VAL* 2.7 17.2 + - + +
1014T TYR 3.7 20.0 - - - +
1015T GLU* 3.6 36.8 - - + +
1031T ALA* 4.4 5.4 - - + -
1081T LEU* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1006 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16T 741 4.5 4.0 + - - -
1004T GLU* 3.7 2.4 - - - +
1005T LEU* 1.3 83.3 - - - +
1007T GLN* 1.3 58.1 + - - -
1012T MET* 3.7 11.3 - - - +
1013T VAL* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1007 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006T GLY* 1.3 72.2 - - - -
1008T GLY* 1.3 66.8 + - - +
1011T GLY 4.3 3.7 - - - +
1012T MET* 3.8 33.5 - - - +
1013T VAL* 4.9 0.8 - - - +
----------------------------------------------------------
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