Contacts of the strand formed by residues 325 - 330 (chain E) in PDB entry 3TMP
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 325 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E VAL* 4.2 21.3 - - + -
232E GLN* 3.6 24.2 - - + -
233E VAL* 3.9 13.9 - - + -
288E MET* 4.9 0.9 - - + +
292E TYR* 3.8 30.1 - - + -
294E ARG* 3.6 40.1 - - + +
295E PRO 2.8 6.7 + - - -
296E VAL* 3.3 28.6 - - + +
297E GLU* 2.9 25.1 + - - +
323E GLU 3.8 0.2 + - - -
324E PRO* 1.3 70.8 - - - +
326E ARG* 1.3 61.2 + - - +
327E VAL* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 326 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E PHE* 3.5 37.8 - - - -
232E GLN* 3.0 17.4 + - - +
297E GLU* 3.1 31.7 + - - +
299E TYR* 3.9 6.5 - - + -
323E GLU* 2.9 35.8 + - - +
324E PRO* 3.6 31.3 + - + +
325E ILE* 1.3 76.6 - - - +
327E VAL* 1.3 65.9 + - - +
337E SER 3.9 0.5 - - - -
338E VAL* 2.9 48.9 + - + +
340E ASN* 3.7 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 327 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E LEU* 4.8 3.8 - - + -
228E ALA* 3.8 24.2 - - + -
229E VAL* 4.6 9.6 - - + -
285E MET* 3.9 20.6 - - + -
296E VAL* 4.9 4.3 - - + -
297E GLU 3.0 15.3 + - - +
298E VAL* 4.1 3.8 - - + -
299E TYR* 2.8 24.8 + - - -
325E ILE* 4.4 16.8 - - + +
326E ARG* 1.3 81.0 - - - +
328E SER* 1.3 58.7 + - - +
335E TYR* 3.7 26.7 - - + -
336E ASN 3.3 9.2 - - - +
338E VAL* 3.5 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 328 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E PHE* 4.3 12.6 - - - -
215E ILE* 4.0 7.6 - - - +
299E TYR* 3.2 9.2 - - - -
327E VAL* 1.3 74.8 - - - +
329E TYR* 1.3 60.2 + - - +
330E HIS* 2.5 34.4 + - - -
335E TYR* 3.1 10.0 - - - -
336E ASN* 2.8 45.9 + - - +
338E VAL* 3.5 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 329 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E GLU* 5.0 0.3 + - - -
203E PHE* 5.6 0.7 - - - -
298E VAL* 4.0 9.2 - - + -
299E TYR 2.8 13.9 + - - +
300E GLN* 3.4 46.5 + - + +
301E TYR 4.7 1.9 + - - -
328E SER* 1.3 72.9 - - - +
330E HIS* 1.3 63.1 + - - +
331E ARG 4.4 0.3 + - - -
332E ASN* 3.1 47.3 + - - -
333E ILE 3.8 2.5 - - - -
334E HIS 3.4 11.2 - - - -
335E TYR* 3.4 36.8 - + + -
40F GLN* 5.1 1.1 - - - -
72F ARG 4.1 3.1 + - - -
73F LEU* 3.3 33.9 - - + -
74F ARG 2.7 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 330 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E GLU* 3.0 36.6 + - - +
203E PHE* 4.5 6.8 - + - -
215E ILE* 3.8 22.0 - - + -
328E SER* 2.5 43.6 + - - -
329E TYR* 1.3 73.3 + - - +
331E ARG* 1.3 79.7 + - - +
332E ASN 2.8 11.4 + - - -
333E ILE* 2.9 11.3 + - - +
334E HIS* 2.8 25.7 + + - +
336E ASN* 3.2 27.6 + - - +
----------------------------------------------------------
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