Contacts of the strand formed by residues 392 - 396 (chain C) in PDB entry 5TT2
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 LEU 392 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C PRO* 4.2 9.2 - - + -
182C THR* 4.4 14.6 - - + -
309C ILE* 5.4 0.2 - - + -
334C THR* 3.7 27.8 - - + -
335C PHE 3.6 4.0 - - - +
336C TYR* 3.2 40.8 - - + +
369C LEU* 3.1 22.3 - - - +
370C PRO* 3.4 30.7 - - + +
388C ILE* 3.9 23.1 - - + -
389C SER* 3.5 14.8 + - - +
391C THR* 1.3 79.0 + - - +
393C ILE* 1.3 66.0 + - - +
394C ARG 4.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C VAL 3.9 1.0 - - - +
334C THR* 3.3 3.6 - - - +
335C PHE* 2.8 64.9 + - + +
337C ILE* 4.6 4.5 - - + -
344C ALA* 4.1 21.8 - - + +
347C PHE* 3.5 34.1 - - + -
348C LEU* 4.4 7.0 - - + -
368C GLU 3.4 18.4 - - - +
369C LEU* 4.5 8.3 - - + -
391C THR 3.9 9.2 - - - +
392C LEU* 1.3 82.0 - - - +
394C ARG* 1.3 62.9 + - - +
395C LEU* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ASN* 3.1 37.8 + - - +
181C PRO* 3.9 13.6 - - + +
332C MET* 3.7 21.3 - - + -
333C VAL 3.6 2.2 - - - +
334C THR* 3.7 18.2 - - - +
357C ALA 4.5 0.8 + - - -
358C VAL 3.1 17.2 + - - -
359C SER 3.0 27.9 + - - -
360C LEU* 3.6 25.5 - - - +
366C LEU* 5.9 0.6 - - - +
367C ALA* 3.8 1.0 - - - -
368C GLU* 3.0 68.5 + - - +
370C PRO* 4.4 2.6 - - + +
392C LEU* 4.8 3.4 - - + -
393C ILE* 1.3 72.3 - - - +
395C LEU* 1.3 66.4 + - - +
396C SER* 4.1 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C VAL* 4.1 14.6 - - + -
299C LEU* 4.0 17.5 - - + -
331C GLY 3.3 0.5 - - - +
332C MET* 3.2 6.9 - - - +
333C VAL* 2.7 46.1 + - + +
335C PHE* 4.0 21.3 - - + -
347C PHE* 5.1 3.4 - - + -
354C PHE* 4.1 19.5 - - + -
366C LEU 3.2 5.4 - - - +
367C ALA* 3.7 28.5 - - + -
393C ILE* 3.8 17.7 - - + -
394C ARG* 1.3 75.7 - - - +
396C SER* 1.3 58.8 + - - +
397C VAL* 3.7 7.4 - - + -
409C LEU* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C HIS* 5.9 0.3 - - - -
331C GLY 3.5 6.3 + - - -
332C MET* 4.6 1.5 - - - +
359C SER 4.8 1.1 - - - -
360C LEU* 3.8 21.3 - - - +
361C GLY* 3.0 32.7 + - - -
362C GLY 5.6 0.2 + - - -
364C GLU 3.8 2.6 - - - +
365C SER* 3.2 2.4 - - - -
366C LEU* 2.7 51.4 + - - +
394C ARG* 4.1 2.7 + - - +
395C LEU* 1.3 70.3 - - - +
397C VAL* 1.3 63.5 + - - +
----------------------------------------------------------
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